From 4df73503d591108b3990db83429fdbfbccc35d7f Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Thu, 12 May 2022 18:07:35 +0100
Subject: [PATCH 001/601] adding easyconfigs: pgplot-5.2.2-GCCcore-11.2.0.eb,
 pgplot-5.2.2-GCCcore-10.3.0.eb

---
 .../p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb   | 51 +++++++++++++++++++
 .../p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb   | 51 +++++++++++++++++++
 2 files changed, 102 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
new file mode 100644
index 00000000000..9aeb3466d7d
--- /dev/null
+++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
@@ -0,0 +1,51 @@
+# Contribution from Imperial College London (UK)
+# Uploaded by J. Sassmannshausen
+
+easyblock = 'CmdCp'
+
+name = 'pgplot'
+version = '5.2.2'
+
+homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/'
+description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, 
+device-independent graphics package for making simple scientific graphs. It is intended 
+for making graphical images of publication quality with minimum effort on the part of 
+the user. For most applications, the program can be device-independent, and the output 
+can be directed to the appropriate device at run time."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+
+source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/']
+sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')]
+patches = ['pgplot-compiler.patch']
+
+checksums = [
+    'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
+    'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace',   # pgplot-compiler.patch
+]
+
+builddependencies = [
+    ('binutils', '2.36.1'),
+]
+
+dependencies = [
+    ('libpng', '1.6.37'),
+    ('zlib', '1.2.11'),
+]
+
+cmds_map = [('.*', './makemake . linux g77_gcc && make ')]
+
+files_to_copy = [
+    (['pgdemo*'], 'bin'),
+    (['libpgplot.a', 'libpgplot.so'], 'lib'),
+    (['grfont.dat'], 'share'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libpgplot.a'],
+    'dirs': []
+}
+
+modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
new file mode 100644
index 00000000000..c9d8a6d0a5a
--- /dev/null
+++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
@@ -0,0 +1,51 @@
+# Contribution from Imperial College London (UK)
+# Uploaded by J. Sassmannshausen
+
+easyblock = 'CmdCp'
+
+name = 'pgplot'
+version = '5.2.2'
+
+homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/'
+description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, 
+device-independent graphics package for making simple scientific graphs. It is intended 
+for making graphical images of publication quality with minimum effort on the part of 
+the user. For most applications, the program can be device-independent, and the output 
+can be directed to the appropriate device at run time."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/']
+sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')]
+patches = ['pgplot-compiler.patch']
+
+checksums = [
+    'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
+    'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace',   # pgplot-compiler.patch
+]
+
+builddependencies = [
+    ('binutils', '2.37'),
+]
+
+dependencies = [
+    ('libpng', '1.6.37'),
+    ('zlib', '1.2.11'),
+]
+
+cmds_map = [('.*', './makemake . linux g77_gcc && make ')]
+
+files_to_copy = [
+    (['pgdemo*'], 'bin'),
+    (['libpgplot.a', 'libpgplot.so'], 'lib'),
+    (['grfont.dat'], 'share'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libpgplot.a'],
+    'dirs': []
+}
+
+modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'}
+
+moduleclass = 'vis'

From a5b97aa7954721ba7800524901c8dcd08264baa6 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Thu, 12 May 2022 21:56:28 +0100
Subject: [PATCH 002/601] missing patchfile added, also building cpgplot stuff
 now

---
 .../p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb   |   9 +-
 .../p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb   |   9 +-
 .../p/pgplot/pgplot-compiler.patch            | 265 ++++++++++++++++++
 3 files changed, 275 insertions(+), 8 deletions(-)
 create mode 100644 easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch

diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
index 9aeb3466d7d..0c13be9dffb 100644
--- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
@@ -21,7 +21,7 @@ patches = ['pgplot-compiler.patch']
 
 checksums = [
     'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
-    'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace',   # pgplot-compiler.patch
+    '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278',   # pgplot-compiler.patch
 ]
 
 builddependencies = [
@@ -33,16 +33,17 @@ dependencies = [
     ('zlib', '1.2.11'),
 ]
 
-cmds_map = [('.*', './makemake . linux g77_gcc && make ')]
+cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')]
 
 files_to_copy = [
     (['pgdemo*'], 'bin'),
-    (['libpgplot.a', 'libpgplot.so'], 'lib'),
+    (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'),
     (['grfont.dat'], 'share'),
+    (['cpgplot.h'], 'include'),
 ]
 
 sanity_check_paths = {
-    'files': ['lib/libpgplot.a'],
+    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'],
     'dirs': []
 }
 
diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
index c9d8a6d0a5a..3bb4f5e1e18 100644
--- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
@@ -21,7 +21,7 @@ patches = ['pgplot-compiler.patch']
 
 checksums = [
     'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
-    'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace',   # pgplot-compiler.patch
+    '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278',   # pgplot-compiler.patch
 ]
 
 builddependencies = [
@@ -33,16 +33,17 @@ dependencies = [
     ('zlib', '1.2.11'),
 ]
 
-cmds_map = [('.*', './makemake . linux g77_gcc && make ')]
+cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')]
 
 files_to_copy = [
     (['pgdemo*'], 'bin'),
-    (['libpgplot.a', 'libpgplot.so'], 'lib'),
+    (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'),
     (['grfont.dat'], 'share'),
+    (['cpgplot.h'], 'include'),
 ]
 
 sanity_check_paths = {
-    'files': ['lib/libpgplot.a'],
+    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'],
     'dirs': []
 }
 
diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch b/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch
new file mode 100644
index 00000000000..58b62e780c4
--- /dev/null
+++ b/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch
@@ -0,0 +1,265 @@
+Patch to make sure that gfortran can be used, also includes EasyBuild specific environment variables
+Some of it is based on the Debian patches
+Author: J. Sassmannshausen (ICL/UK)
+diff --git a/pgplot.orig/drivers/pndriv.c b/pgplot/drivers/pndriv.c
+index 2b2f87d..63fa246 100644
+--- a/pgplot.orig/drivers/pndriv.c
++++ b/pgplot/drivers/pndriv.c
+@@ -222,7 +222,7 @@ static void write_image_file(DeviceData *dev) {
+ 	return;
+   }
+ 
+-  if (setjmp(png_ptr->jmpbuf)) { /* not really sure what I'm doing here... */
++  if (setjmp(png_jmpbuf(png_ptr))) { /* not really sure what I'm doing here... */
+ 	fprintf(stderr,"%s: error in libpng while writing file %s, plotting disabled\n", png_ident, filename);
+ 	png_destroy_write_struct(&png_ptr,&info_ptr);
+ 	dev->error = true;
+diff --git a/pgplot.orig/drivers.list b/pgplot/drivers.list
+index 11108bb..b6ff758 100644
+--- a/pgplot.orig/drivers.list
++++ b/pgplot/drivers.list
+@@ -3,48 +3,50 @@
+ ! To configure PGPLOT, ensure that drivers you do not want are
+ ! commented out (place ! in column 1). N.B. Many device-drivers are
+ ! available on selected operating systems only.
++! Modified by Gopal Narayanan <gopal@debian.org> for debian Jul 6, 2001
+ !------------------------------------------------------------------------------
+ ! File       Code       Description                                Restrictions
+ ! BCDRIV 0 /BCANON    Canon Laser printer (bitmap version), landscape
+ ! CADRIV 0 /CANON     Canon Laser printer, LBP-8/A2, landscape
+ ! CCDRIV 0 /CCP       DEC LJ250 Color Companion printer
+-! CGDRIV 1 /CGM       CGM metafile, indexed colour selection            C
+-! CGDRIV 2 /CGMD      CGM metafile, direct colour selection             C
++ CGDRIV 1 /CGM       CGM metafile, indexed colour selection            C
++ CGDRIV 2 /CGMD      CGM metafile, direct colour selection             C
+ ! CWDRIV 0 /CW6320    Gould/Bryans Colourwriter 6320 pen plotter	Std F77
+ ! EPDRIV 0 /EPSON     Epson FX100 dot matrix printer
+ ! EXDRIV 1 /EXCL      Talaris/EXCL printers, landscape
+ ! EXDRIV 2 /EXCL      Talaris/EXCL printers, portrait
+ ! GCDRIV 0 /GENICOM   Genicom 4410 dot-matrix printer, landscape
+ !             Caution: use of GIDRIV may require a license from Unisys:
+-! GIDRIV 1 /GIF       GIF-format file, landscape
+-! GIDRIV 2 /VGIF      GIF-format file, portrait
+-! GLDRIV 1 /HPGL      Hewlett-Packard HP-GL plotters, landscape		Std F77
+-! GLDRIV 2 /VHPGL     Hewlett-Packard HP-GL plotters, portrait		Std F77
++!             Since Unisys patent has expired allowing now. <June 16, 2006>
++ GIDRIV 1 /GIF       GIF-format file, landscape
++ GIDRIV 2 /VGIF      GIF-format file, portrait
++ GLDRIV 1 /HPGL      Hewlett-Packard HP-GL plotters, landscape		Std F77
++ GLDRIV 2 /VHPGL     Hewlett-Packard HP-GL plotters, portrait		Std F77
+ ! GODRIV 0 /GOC       GOC Sigma T5670 terminal				VMS 
+ ! GVDRIV 0 /GVENICOM  Genicom 4410 dot-matrix printer, portrait
+-! HGDRIV 0 /HPGL2     Hewlett-Packard graphics language
++ HGDRIV 0 /HPGL2     Hewlett-Packard graphics language
+ ! HIDRIV 0 /HIDMP     Houston Instruments HIDMP pen plotter
+ ! HJDRIV 0 /HJ        Hewlett-Packard Desk/Laserjet printer
+-! HPDRIV 0 /HP7221    Hewlett-Packard HP7221 pen plotter		Std F77
++ HPDRIV 0 /HP7221    Hewlett-Packard HP7221 pen plotter		Std F77
+ ! LADRIV 0 /LA50      Dec LA50 and other sixel printers
+ ! LJDRIV 0 /LJ        Hewlett-Packard LaserJet printers                 VMS
+ ! LSDRIV 1 /LIPS2     Canon LaserShot printer (landscape)
+ ! LSDRIV 2 /VLIPS2    Canon LaserShot printer (portrait)
+ ! LNDRIV 0 /LN03      Dec LN03-PLUS Laser printer (landscape)           VMS
+ ! LVDRIV 0 /LVN03     Dec LN03-PLUS Laser printer (portrait)            VMS
+-! LXDRIV 0 /LATEX     LaTeX picture environment
++ LXDRIV 0 /LATEX     LaTeX picture environment
+ ! MFDRIV 0 /FILE      PGPLOT graphics metafile
+ ! NEDRIV 0 /NEXT      Computers running NeXTstep operating system
+   NUDRIV 0 /NULL      Null device (no output)				Std F77
+-! PGDRIV 0 /PGMF      PGPLOT metafile (new format, experimental)        Std F77
+-! PNDRIV 1 /PNG       Portable Network Graphics file                    C
+-! PNDRIV 2 /TPNG      Portable Network Graphics file - transparent background C
++  PGDRIV 0 /PGMF      PGPLOT metafile (new format, experimental)        Std F77
++ PNDRIV 1 /PNG       Portable Network Graphics file                    C
++ PNDRIV 2 /TPNG      Portable Network Graphics file - transparent background C
+ ! PPDRIV 1 /PPM       Portable Pixel Map file, landscape
+ ! PPDRIV 2 /VPPM      Portable PIxel Map file, portrait
+-! PSDRIV 1 /PS        PostScript printers, monochrome, landscape	Std F77
+-! PSDRIV 2 /VPS       Postscript printers, monochrome, portrait		Std F77
+-! PSDRIV 3 /CPS       PostScript printers, color, landscape		Std F77
+-! PSDRIV 4 /VCPS      PostScript printers, color, portrait		Std F77
++ PSDRIV 1 /PS        PostScript printers, monochrome, landscape	Std F77
++ PSDRIV 2 /VPS       Postscript printers, monochrome, portrait		Std F77
++ PSDRIV 3 /CPS       PostScript printers, color, landscape		Std F77
++ PSDRIV 4 /VCPS      PostScript printers, color, portrait		Std F77
+ ! PXDRIV 0 /PRINTRONI Printronix P300 or P600 dot-matrix printer
+ ! QMDRIV 1 /QMS       QUIC devices (QMS and Talaris), landscape		Std F77
+ ! QMDRIV 2 /VQMS      QUIC devices (QMS and Talaris), portrait		Std F77
+diff --git a/pgplot.orig/makemake b/pgplot/makemake
+index e48455e..93b9985 100755
+--- a/pgplot.orig/makemake
++++ b/pgplot/makemake
+@@ -658,6 +658,8 @@ CPGPLOT_LIB=$CPGPLOT_LIB
+ #
+ SHARED_LIB=$SHARED_LIB
+ SHARED_LD=$SHARED_LD
++SHARED_LD_PGPLOT_OPTS=$SHARED_LD_PGPLOT_OPTS
++SHARED_LD_CPGPLOT_OPTS=$SHARED_LD_CPGPLOT_OPTS
+ #
+ # The libraries that the shared PGPLOT library depends upon.
+ # This is for systems that allow one to specify what libraries
+@@ -667,6 +669,7 @@ SHARED_LD=$SHARED_LD
+ # libraries when they link their executables.
+ #
+ SHARED_LIB_LIBS=$SHARED_LIB_LIBS
++SHARED_LIB_CPGPLOT_LIBS=$SHARED_LIB_CPGPLOT_LIBS
+ #
+ # Ranlib command if required
+ #
+@@ -806,7 +809,8 @@ grexec.o: grexec.f
+ # libraries.
+ #-----------------------------------------------------------------------
+ 
+-lib : libpgplot.a $(SHARED_LIB)
++#lib : libpgplot.a $(SHARED_LIB)
++lib : libpgplot.a
+ 
+ libpgplot.a : $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \
+ 	   $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES)
+@@ -816,6 +820,16 @@ libpgplot.a : $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \
+ 		$(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq`
+ 	$(RANLIB) libpgplot.a
+ 
++#shared: $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \
++#	   $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES)
++#	   $(SHARED_LD)
++
++shared: $(PG_ROUTINES) $(PG_NON_STANDARD) \
++	$(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES)
++	$(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \
++	$(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \
++	$(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS)
++
+ EOD
+ 
+ # Emit the shared library dependency if requested.
+@@ -824,7 +838,7 @@ if test -n "$SHARED_LIB" -a -n "$SHARED_LD"; then
+ cat >> makefile << \EOD
+ $(SHARED_LIB): $(PG_ROUTINES) $(PG_NON_STANDARD) \
+ 	$(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES)
+-	$(SHARED_LD) `ls $(PG_ROUTINES) \
++	$(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \
+ 	$(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \
+ 	$(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS)
+ EOD
+@@ -1019,13 +1033,14 @@ EOD
+ 
+ cat >> makefile << \EOD
+ 
++DEB_HOST_MULTIARCH=$(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
++
+ # Miscellaneous include files required by drivers
+ 
+ griv00.o : $(DRVDIR)/gadef.h $(DRVDIR)/gmdef.h $(DRVDIR)/gphdef.h
+ grivas.o : $(DRVDIR)/gadef.h
+ grtv00.o : $(DRVDIR)/imdef.h
+ pgxwin.o : $(DRVDIR)/pgxwin.h
+-pndriv.o : ./png.h ./pngconf.h ./zlib.h ./zconf.h
+ 
+ x2driv.o figdisp_comm.o: $(DRVDIR)/commands.h
+ 
+@@ -1039,6 +1054,8 @@ cpg:	libcpgplot.a cpgplot.h cpgdemo
+ 	@echo 'will be needed.'
+ 	@echo ' '
+ 
++cpg-shared: libcpgplot.so
++
+ pgbind: $(SRC)/cpg/pgbind.c
+ 	$(CCOMPL) $(CFLAGC) $(SRC)/cpg/pgbind.c -o pgbind
+ 
+@@ -1050,6 +1067,13 @@ libcpgplot.a cpgplot.h: $(PG_SOURCE) pgbind
+ 	$(RANLIB) libcpgplot.a
+ 	rm -f cpg*.o
+ 
++libcpgplot.so: $(PG_SOURCE) pgbind
++	./pgbind $(PGBIND_FLAGS) -w $(PG_SOURCE)
++	$(CCOMPL) -c $(CFLAGC) cpg*.c
++	rm -f cpg*.c
++	$(SHARED_LD) $(SHARED_LD_CPGPLOT_OPTS) cpg*.o $(SHARED_LIB_CPGPLOT_LIBS)
++	rm -f cpg*.o
++
+ cpgdemo: cpgplot.h $(SRC)/cpg/cpgdemo.c libcpgplot.a
+ 	$(CCOMPL) $(CFLAGD) -c -I. $(SRC)/cpg/cpgdemo.c
+ 	$(FCOMPL) -o cpgdemo cpgdemo.o $(CPGPLOT_LIB) $(LIBS)
+diff --git a/pgplot.orig/sys_linux/g77_gcc.conf b/pgplot/sys_linux/g77_gcc.conf
+index d6b73e6..b3905b0 100644
+--- a/pgplot.orig/sys_linux/g77_gcc.conf
++++ b/pgplot/sys_linux/g77_gcc.conf
+@@ -1,11 +1,11 @@
+-# The GNU g77 FORTRAN compiler and Gnu gcc C compiler on an elf-system.
++# The GNU gfortran FORTRAN compiler and Gnu gcc C compiler on an elf-system.
+ #-----------------------------------------------------------------------
+ 
+ # Optional: Needed by XWDRIV (/xwindow and /xserve) and
+ #           X2DRIV (/xdisp and /figdisp).
+ # The arguments needed by the C compiler to locate X-window include files.
+  
+-   XINCL="-I/usr/X11R6/include"
++   XINCL="-I${EBROOTLIBPNG}/include -I${BROOTZLIB}/include"
+ 
+ # Optional: Needed by XMDRIV (/xmotif).
+ # The arguments needed by the C compiler to locate Motif, Xt and
+@@ -34,13 +34,13 @@
+ # Mandatory.
+ # The FORTRAN compiler to use.
+  
+-   FCOMPL="g77"
++   FCOMPL="gfortran"
+ 
+ # Mandatory.
+ # The FORTRAN compiler flags to use when compiling the pgplot library.
+ # (NB. makemake prepends -c to $FFLAGC where needed)
+  
+-   FFLAGC="-u -Wall -fPIC -O"
++   FFLAGC="-u -Wall -fPIC -O3 -std=legacy "
+ 
+ # Mandatory.
+ # The FORTRAN compiler flags to use when compiling fortran demo programs.
+@@ -57,12 +57,12 @@
+ # Mandatory.
+ # The C compiler flags to use when compiling the pgplot library.
+  
+-   CFLAGC="-Wall -fPIC -DPG_PPU -O"
++   CFLAGC="-Wall -fPIC -DPG_PPU -O3"
+ 
+ # Mandatory.
+ # The C compiler flags to use when compiling C demo programs.
+  
+-   CFLAGD="-Wall -O"
++   CFLAGD="-Wall -O3"
+ 
+ # Optional: Only needed if the cpgplot library is to be compiled.
+ # The flags to use when running pgbind to create the C pgplot wrapper
+@@ -74,7 +74,7 @@
+ # The library-specification flags to use when linking normal pgplot
+ # demo programs.
+  
+-   LIBS="-L/usr/X11R6/lib -lX11"
++   LIBS="-L${EBROOTLIBPNG}/lib -lpng"
+ 
+ # Optional: Needed by XMDRIV (/xmotif).
+ # The library-specification flags to use when linking motif
+@@ -108,7 +108,11 @@
+ # Optional: Needed if SHARED_LIB is set.
+ # How to create a shared library from a trailing list of object files.
+  
+-   SHARED_LD="gcc -shared  -o $SHARED_LIB"
++   SHARED_LD_PGPLOT_OPTS="-o $SHARED_LIB -Wl,-soname,libpgplot.so.\$(VM)"
++
++   SHARED_LD_CPGPLOT_OPTS="-o libcpgplot.so -Wl,-soname,libcpgplot.so.\$(VM)"
++
++   SHARED_LD="gfortran -shared"
+ 
+ # Optional:
+ # On systems such as Solaris 2.x, that allow specification of the
+@@ -117,7 +121,9 @@
+ # library-specification flags used to specify these libraries to
+ # $SHARED_LD
+  
+-   SHARED_LIB_LIBS=""
++   SHARED_LIB_LIBS="-L/usr/X11R6/lib -lX11 -lpng -lc -lgfortran"
++
++   SHARED_LIB_CPGPLOT_LIBS="-L. -lpgplot"
+ 
+ # Optional:
+ # Compiler name used on Next systems to compile objective-C files.

From 30e8a89eee923bac081f83d47272d4c54f84ed69 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Thu, 12 May 2022 22:56:04 +0100
Subject: [PATCH 003/601] missing X11 added, shared libs removed as there is a
 problem

---
 .../easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb      | 5 +++--
 .../easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb      | 5 +++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
index 0c13be9dffb..b95eada0090 100644
--- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
@@ -31,13 +31,14 @@ builddependencies = [
 dependencies = [
     ('libpng', '1.6.37'),
     ('zlib', '1.2.11'),
+    ('X11', '20210518'),
 ]
 
-cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')]
+cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')]
 
 files_to_copy = [
     (['pgdemo*'], 'bin'),
-    (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'),
+    (['libpgplot.a', 'libcpgplot.a'], 'lib'),
     (['grfont.dat'], 'share'),
     (['cpgplot.h'], 'include'),
 ]
diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
index 3bb4f5e1e18..fcfae8351cd 100644
--- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
@@ -31,13 +31,14 @@ builddependencies = [
 dependencies = [
     ('libpng', '1.6.37'),
     ('zlib', '1.2.11'),
+    ('X11', '20210802'),
 ]
 
-cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')]
+cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')]
 
 files_to_copy = [
     (['pgdemo*'], 'bin'),
-    (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'),
+    (['libpgplot.a', 'libcpgplot.a'], 'lib'),
     (['grfont.dat'], 'share'),
     (['cpgplot.h'], 'include'),
 ]

From 9687ec6af2b338ed3cb07d3693dd624a53036776 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Thu, 12 May 2022 23:31:47 +0100
Subject: [PATCH 004/601] adding easyconfigs: wcslib-7.11-GCC-11.2.0.eb

---
 .../w/wcslib/wcslib-7.11-GCC-11.2.0.eb        | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb
new file mode 100644
index 00000000000..7a4add2a792
--- /dev/null
+++ b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb
@@ -0,0 +1,43 @@
+# Contribution from Imperial College London (UK)
+# Uploaded by J. Sassmannshausen
+
+easyblock = 'ConfigureMake'
+
+name = 'wcslib'
+version = '7.11'
+
+homepage = 'https://www.atnf.csiro.au/people/mcalabre/WCS/'
+description = """The FITS "World Coordinate System" (WCS) standard defines keywords 
+and usage that provide for the description of astronomical coordinate systems in a 
+FITS image header."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['ftp://ftp.atnf.csiro.au/pub/software/wcslib/']
+sources = ['%(name)s-%(version)s.tar.bz2']
+checksums = ['46befbfdf50cd4953896676a7d570094dc7661e2ae9677b092e7fb13cee3da5f']
+
+builddependencies = [
+    ('binutils', '2.37'),
+    ('M4', '1.4.19'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('CFITSIO', '3.49'),
+    ('pgplot', '5.2.2'),
+    ('X11', '20210802'),
+]
+
+configure_cmd = './configure --with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include '
+configure_cmd += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include '
+
+sanity_check_paths = {
+    'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-7.11.a', 'lib/libpgsbox.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+runtest = 'wcsgrid --help'
+
+moduleclass = 'geo'

From 5fe98e0e97aa50eba0c9f769a1eea55be615f722 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Thu, 12 May 2022 23:49:06 +0100
Subject: [PATCH 005/601] sanity-check-command removed as it does not work as
 intended

---
 easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb
index 7a4add2a792..8025066e463 100644
--- a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb
@@ -38,6 +38,4 @@ sanity_check_paths = {
     'dirs': ['include'],
 }
 
-runtest = 'wcsgrid --help'
-
 moduleclass = 'geo'

From 2391e5f18f155dfdc94200199b3cbdbbeff82123 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Fri, 13 May 2022 11:49:54 +0100
Subject: [PATCH 006/601] adding easyconfigs: casacore-3.4.0-foss-2021b.eb

---
 .../c/casacore/casacore-3.4.0-foss-2021b.eb   | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb

diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
new file mode 100644
index 00000000000..8b35c61878f
--- /dev/null
+++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
@@ -0,0 +1,43 @@
+# Contribution from Imperial College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'CMakeMake'
+
+name = 'casacore'
+version = '3.4.0'
+
+homepage = 'https://github.com/casacore/casacore'
+description = "A suite of C++ libraries for radio astronomy data processing."
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = ['https://github.com/casacore/casacore/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = [
+    '31f02ad2e26f29bab4a47a2a69e049d7bc511084a0b8263360e6157356f92ae1',  # v3.4.0.tar.gz
+]
+
+builddependencies = [
+    ('binutils', '2.37'),
+    ('CMake', '3.22.1'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.7.6'),
+]
+
+dependencies = [
+    ('CFITSIO', '3.49'),
+    ('wcslib', '7.11'),
+    ('HDF5', '1.12.1'),
+    ('SciPy-bundle', '2021.10'),
+    ('Boost.Python', '1.77.0'),
+    ('ncurses', '6.2'),
+]
+
+configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev '
+
+sanity_check_paths = {
+    'files': [('lib/libcasa_casa.%s', 'lib/libcasa_mirlib.%s' % SHLIB_EXT, 'lib64/libcasa_ms.%s' % SHLIB_EXT)],
+    'dirs': ['include/casacore'],
+}
+
+moduleclass = 'lib'

From 842cbf1e041be888419207165ae2b966da1f83e8 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 16 May 2022 15:38:54 +0100
Subject: [PATCH 007/601] shared libs created, EC linted, name changed to
 upper-cases

---
 .../PGPLOT-5.2.2-GCCcore-10.3.0.eb}            | 18 ++++++++++++------
 .../PGPLOT-5.2.2-GCCcore-11.2.0.eb}            | 18 ++++++++++++------
 .../pgplot-compiler-pgplot522.patch}           |  4 ++--
 3 files changed, 26 insertions(+), 14 deletions(-)
 rename easybuild/easyconfigs/p/{pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb => PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb} (66%)
 rename easybuild/easyconfigs/p/{pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb => PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb} (66%)
 rename easybuild/easyconfigs/p/{pgplot/pgplot-compiler.patch => PGPLOT/pgplot-compiler-pgplot522.patch} (98%)

diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
similarity index 66%
rename from easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
rename to easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
index b95eada0090..505de914edf 100644
--- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
@@ -3,7 +3,7 @@
 
 easyblock = 'CmdCp'
 
-name = 'pgplot'
+name = 'PGPLOT'
 version = '5.2.2'
 
 homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/'
@@ -16,12 +16,12 @@ can be directed to the appropriate device at run time."""
 toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
 
 source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/']
-sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')]
-patches = ['pgplot-compiler.patch']
+sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')]
+patches = ['pgplot-compiler-pgplot522.patch']
 
 checksums = [
     'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
-    '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278',   # pgplot-compiler.patch
+    'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec',   # pgplot-compiler-pgplot522.patch
 ]
 
 builddependencies = [
@@ -34,15 +34,21 @@ dependencies = [
     ('X11', '20210518'),
 ]
 
-cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')]
+cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')]
 
 files_to_copy = [
     (['pgdemo*'], 'bin'),
-    (['libpgplot.a', 'libcpgplot.a'], 'lib'),
+    (['libpgplot.*', 'libcpgplot.*'], 'lib'),
     (['grfont.dat'], 'share'),
     (['cpgplot.h'], 'include'),
 ]
 
+postinstallcmds = [
+    # create symlinks
+    "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && "
+    " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so"
+]
+
 sanity_check_paths = {
     'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'],
     'dirs': []
diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
similarity index 66%
rename from easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
rename to easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
index fcfae8351cd..8bf72fe23f5 100644
--- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
@@ -3,7 +3,7 @@
 
 easyblock = 'CmdCp'
 
-name = 'pgplot'
+name = 'PGPLOT'
 version = '5.2.2'
 
 homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/'
@@ -16,12 +16,12 @@ can be directed to the appropriate device at run time."""
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
 source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/']
-sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')]
-patches = ['pgplot-compiler.patch']
+sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')]
+patches = ['pgplot-compiler-pgplot522.patch']
 
 checksums = [
     'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
-    '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278',   # pgplot-compiler.patch
+    'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec',   # pgplot-compiler-pgplot522.patch
 ]
 
 builddependencies = [
@@ -34,15 +34,21 @@ dependencies = [
     ('X11', '20210802'),
 ]
 
-cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')]
+cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')]
 
 files_to_copy = [
     (['pgdemo*'], 'bin'),
-    (['libpgplot.a', 'libcpgplot.a'], 'lib'),
+    (['libpgplot.*', 'libcpgplot.*'], 'lib'),
     (['grfont.dat'], 'share'),
     (['cpgplot.h'], 'include'),
 ]
 
+postinstallcmds = [
+    # create symlinks
+    "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && "
+    " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so"
+]
+
 sanity_check_paths = {
     'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'],
     'dirs': []
diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch b/easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch
similarity index 98%
rename from easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch
rename to easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch
index 58b62e780c4..d8073c05f6f 100644
--- a/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch
+++ b/easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch
@@ -244,9 +244,9 @@ index d6b73e6..b3905b0 100644
  # How to create a shared library from a trailing list of object files.
   
 -   SHARED_LD="gcc -shared  -o $SHARED_LIB"
-+   SHARED_LD_PGPLOT_OPTS="-o $SHARED_LIB -Wl,-soname,libpgplot.so.\$(VM)"
++   SHARED_LD_PGPLOT_OPTS="-o $SHARED_LIB.5.2.2 -Wl,-soname,libpgplot.so.5.2.2"
 +
-+   SHARED_LD_CPGPLOT_OPTS="-o libcpgplot.so -Wl,-soname,libcpgplot.so.\$(VM)"
++   SHARED_LD_CPGPLOT_OPTS="-o libcpgplot.so.5.2.2 -Wl,-soname,libcpgplot.so.5.2.2"
 +
 +   SHARED_LD="gfortran -shared"
  

From be28de92db8d3365ed68913525c8f0312d279159 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 16 May 2022 16:08:28 +0100
Subject: [PATCH 008/601] PGPLOT name updated, configopts used instead of
 configure_cmd, name changed to upper case and source-name updated

---
 .../WCSLIB-7.11-GCC-11.2.0.eb}                         | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)
 rename easybuild/easyconfigs/w/{wcslib/wcslib-7.11-GCC-11.2.0.eb => WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb} (76%)

diff --git a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb
similarity index 76%
rename from easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb
rename to easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb
index 8025066e463..782f085864d 100644
--- a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb
@@ -3,7 +3,7 @@
 
 easyblock = 'ConfigureMake'
 
-name = 'wcslib'
+name = 'WCSLIB'
 version = '7.11'
 
 homepage = 'https://www.atnf.csiro.au/people/mcalabre/WCS/'
@@ -15,7 +15,7 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'}
 toolchainopts = {'pic': True}
 
 source_urls = ['ftp://ftp.atnf.csiro.au/pub/software/wcslib/']
-sources = ['%(name)s-%(version)s.tar.bz2']
+sources = [SOURCELOWER_TAR_BZ2]
 checksums = ['46befbfdf50cd4953896676a7d570094dc7661e2ae9677b092e7fb13cee3da5f']
 
 builddependencies = [
@@ -26,12 +26,12 @@ builddependencies = [
 
 dependencies = [
     ('CFITSIO', '3.49'),
-    ('pgplot', '5.2.2'),
+    ('PGPLOT', '5.2.2'),
     ('X11', '20210802'),
 ]
 
-configure_cmd = './configure --with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include '
-configure_cmd += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include '
+configopts = '--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include '
+configopts += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include '
 
 sanity_check_paths = {
     'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-7.11.a', 'lib/libpgsbox.%s' % SHLIB_EXT],

From 34716dd9ab1db7ddc7c4cba2a1b63661d2e95eaa Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 16 May 2022 16:32:25 +0100
Subject: [PATCH 009/601] wcslib changed to WCSLIB

---
 easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
index 8b35c61878f..a2ee8e062e5 100644
--- a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
@@ -26,7 +26,7 @@ builddependencies = [
 
 dependencies = [
     ('CFITSIO', '3.49'),
-    ('wcslib', '7.11'),
+    ('WCSLIB', '7.11'),
     ('HDF5', '1.12.1'),
     ('SciPy-bundle', '2021.10'),
     ('Boost.Python', '1.77.0'),

From f0408566532cc65b72de3b17ec2140d545cb00d6 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Wed, 25 May 2022 11:04:13 -0700
Subject: [PATCH 010/601] spektral 1.1.0

---
 .../spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb  | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb

diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
new file mode 100644
index 00000000000..b76774997e1
--- /dev/null
+++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
@@ -0,0 +1,38 @@
+# easybuild easyconfig
+#
+# John Dey <jfdey@fredhutch.org>
+#
+# Fred Hutchinson Cancer Center - Seattle Washington - US
+#
+easyblock = 'PythonPackage'
+
+name = 'spektral'
+version = '1.1.0'
+local_cuda_suffix = '-CUDA-%(cudaver)s'
+versionsuffix = local_cuda_suffix
+
+homepage = 'https://github.com/danielegrattarola/spektral'
+description = """Spektral is a Python library for graph deep learning. The main goal of this
+ project is to provide a simple but flexible framework for creating graph neural networks (GNNs)."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3b73549f213f0d36a0bf67595aa3c4d84efb8e0e40d71aeaa1d78ea896245222']
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('lxml', '4.6.3'),
+    ('SciPy-bundle', '2021.10'),
+    ('networkx', '2.6.3'),
+    ('tqdm', '4.62.3'),
+    ('scikit-learn', '1.0.1'),
+    ('CUDA', '11.4.1', '', True),
+    ('TensorFlow', '2.7.1', '-CUDA-%(cudaver)s'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 42476b417a0d7ccaa7d7b823a2a190bf66beed16 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 6 Jun 2022 15:09:25 +0100
Subject: [PATCH 011/601] OpenMPI and DATA_DIR added. The latter is
 deliberately empty so users can define that at runtime

---
 .../easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb   | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
index a2ee8e062e5..8c95efa1c75 100644
--- a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
@@ -7,7 +7,10 @@ name = 'casacore'
 version = '3.4.0'
 
 homepage = 'https://github.com/casacore/casacore'
-description = "A suite of C++ libraries for radio astronomy data processing."
+description = """A suite of C++ libraries for radio astronomy data processing.
+The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime.
+Thus user's can update them.
+"""
 
 toolchain = {'name': 'foss', 'version': '2021b'}
 
@@ -33,7 +36,8 @@ dependencies = [
     ('ncurses', '6.2'),
 ]
 
-configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev '
+configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev -DDATA_DIR=%(installdir)s/data '
+configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON '
 
 sanity_check_paths = {
     'files': [('lib/libcasa_casa.%s', 'lib/libcasa_mirlib.%s' % SHLIB_EXT, 'lib64/libcasa_ms.%s' % SHLIB_EXT)],

From c9a77588b2e519f31e4f2abd7888ba4cb2a653db Mon Sep 17 00:00:00 2001
From: John Dey <john@fuzzdog.com>
Date: Thu, 16 Jun 2022 10:37:53 -0700
Subject: [PATCH 012/601] Update
 easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb

Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com>
---
 .../s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb        | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
index b76774997e1..32f3f69432e 100644
--- a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
@@ -8,8 +8,7 @@ easyblock = 'PythonPackage'
 
 name = 'spektral'
 version = '1.1.0'
-local_cuda_suffix = '-CUDA-%(cudaver)s'
-versionsuffix = local_cuda_suffix
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/danielegrattarola/spektral'
 description = """Spektral is a Python library for graph deep learning. The main goal of this

From d16bda6e62de21bf6e395f72132a39bf0c8f1d64 Mon Sep 17 00:00:00 2001
From: John Dey <john@fuzzdog.com>
Date: Thu, 16 Jun 2022 10:38:00 -0700
Subject: [PATCH 013/601] Update
 easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb

Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com>
---
 .../s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
index 32f3f69432e..171697664e9 100644
--- a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
@@ -27,7 +27,7 @@ dependencies = [
     ('tqdm', '4.62.3'),
     ('scikit-learn', '1.0.1'),
     ('CUDA', '11.4.1', '', True),
-    ('TensorFlow', '2.7.1', '-CUDA-%(cudaver)s'),
+    ('TensorFlow', '2.7.1', versionsuffix),
 ]
 
 download_dep_fail = True

From a7ac8d3b4309fb728234e31a0ea2416298fc8780 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Fri, 8 Jul 2022 14:05:03 +0200
Subject: [PATCH 014/601] adding easyconfigs: Raven-1.8.1-GCC-11.2.0.eb

---
 .../r/Raven/Raven-1.8.1-GCC-11.2.0.eb         | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
new file mode 100644
index 00000000000..a47333637b5
--- /dev/null
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -0,0 +1,46 @@
+easyblock = "CMakeNinja"
+
+name = "Raven"
+version = "1.8.1"
+
+homepage = "https://github.com/lbcb-sci/raven"
+description = "Raven is a de novo genome assembler for long uncorrected reads."
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ["https://github.com/lbcb-sci/raven/archive/refs/tags/"]
+sources = ["%(version)s.tar.gz"]
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+    ('Ninja', '1.10.2'),
+]
+
+configopts = ['-DRAVEN_BUILD_EXE=1 -G Ninja ']
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('zlib', '1.2.11'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'],
+        'sources': ['%(version)s.tar.gz'],
+        'use_pip': True,
+        'download_dep_fail': True,
+        'modulename': 'ravenpy',
+    })
+]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ["/"]
+}
+
+sanity_check_commands = ["pip check"]
+
+moduleclass = "bio"
\ No newline at end of file

From 4c1f146463e13af22adba01dcbb4567336291a90 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Fri, 8 Jul 2022 14:11:28 +0200
Subject: [PATCH 015/601] Fixed sanity_check_paths

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index a47333637b5..f50eb573e34 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -37,8 +37,8 @@ exts_list = [
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 
 sanity_check_paths = {
-    'files': [],
-    'dirs': ["/"]
+    'files': ['bin/raven'],
+    'dirs': []
 }
 
 sanity_check_commands = ["pip check"]

From 50a3d6bec53c4cad306b035007eca9bd181a7f69 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Fri, 8 Jul 2022 14:37:53 +0200
Subject: [PATCH 016/601] Added new line to the end of file

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index f50eb573e34..8a170faf9ef 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -43,4 +43,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ["pip check"]
 
-moduleclass = "bio"
\ No newline at end of file
+moduleclass = "bio"

From 59e6754e6a1f7cd65f01750fedeb836a7eb3a5d9 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Fri, 8 Jul 2022 16:22:18 +0200
Subject: [PATCH 017/601] Added checksums

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index 8a170faf9ef..0665537f846 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -10,6 +10,7 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'}
 
 source_urls = ["https://github.com/lbcb-sci/raven/archive/refs/tags/"]
 sources = ["%(version)s.tar.gz"]
+checksums = ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06']
 
 builddependencies = [
     ('CMake', '3.22.1'),
@@ -26,12 +27,13 @@ dependencies = [
 exts_defaultclass = 'PythonPackage'
 exts_list = [
     (name, version, {
+        'download_dep_fail': True,
+        'modulename': 'ravenpy',
         'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'],
         'sources': ['%(version)s.tar.gz'],
         'use_pip': True,
-        'download_dep_fail': True,
-        'modulename': 'ravenpy',
-    })
+        'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'],
+    }),
 ]
 
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}

From 81692ca6ecee52e530c3b1a4861984ffae66f6af Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Tue, 12 Jul 2022 17:00:29 +0200
Subject: [PATCH 018/601] Added exts_default_options

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index 0665537f846..09bd28b9332 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -25,13 +25,17 @@ dependencies = [
 ]
 
 exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+}
+
 exts_list = [
     (name, version, {
-        'download_dep_fail': True,
         'modulename': 'ravenpy',
         'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'],
         'sources': ['%(version)s.tar.gz'],
-        'use_pip': True,
         'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'],
     }),
 ]

From ac94590288cfb7f7d5123a9b6aef4aa76d38873b Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Tue, 12 Jul 2022 17:12:02 +0200
Subject: [PATCH 019/601] Specified the maximum number of concurrent processes
 to use when building

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index 09bd28b9332..6133c17411e 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -17,6 +17,7 @@ builddependencies = [
     ('Ninja', '1.10.2'),
 ]
 
+preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && "
 configopts = ['-DRAVEN_BUILD_EXE=1 -G Ninja ']
 
 dependencies = [

From f05a609438ad6881e1fbf0d0b45f604dd2ee4367 Mon Sep 17 00:00:00 2001
From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com>
Date: Mon, 18 Jul 2022 16:12:54 +0200
Subject: [PATCH 020/601] Added sanity check for binary

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index 6133c17411e..ff53344aa8a 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -48,6 +48,9 @@ sanity_check_paths = {
     'dirs': []
 }
 
-sanity_check_commands = ["pip check"]
+sanity_check_commands = [
+    "pip check",
+    "raven --help"
+]
 
 moduleclass = "bio"

From c274538476002fe9412bef331761c292e3186fc4 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 3 Aug 2022 15:40:38 +0100
Subject: [PATCH 021/601] Added sanity check for shared libs

---
 easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb | 2 +-
 easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
index 505de914edf..e71115ce833 100644
--- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
@@ -50,7 +50,7 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'],
+    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT],
     'dirs': []
 }
 
diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
index 8bf72fe23f5..3ffb0eb70e6 100644
--- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
@@ -50,7 +50,7 @@ postinstallcmds = [
 ]
 
 sanity_check_paths = {
-    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'],
+    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT],
     'dirs': []
 }
 

From ff5ba6f3f3fcae57568c351e9edf41fac417786f Mon Sep 17 00:00:00 2001
From: alin m elena <alinm.elena@gmail.com>
Date: Tue, 9 Aug 2022 12:55:31 +0100
Subject: [PATCH 022/601] [cp2k] add cp2k 9.1 and 2022.1 to foss 2022a

---
 .../c/CP2K/CP2K-2022.1-foss-2022a.eb          | 40 +++++++++++++++++++
 .../easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb | 39 ++++++++++++++++++
 2 files changed, 79 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb
new file mode 100644
index 00000000000..3521d55a090
--- /dev/null
+++ b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb
@@ -0,0 +1,40 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'CP2K'
+version = '2022.1'
+
+homepage = 'https://www.cp2k.org/'
+description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular
+ simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different
+ methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and
+ classical pair and many-body potentials. """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b']
+
+#                https://github.com/cp2k/cp2k/releases/download/v2022.1/cp2k-2022.1.tar.bz2
+dependencies = [
+    ('Libint', '2.6.0', '-lmax-6-cp2k'),
+    ('libxc', '5.2.3'),
+    ('libxsmm', '1.17'),
+    ('FFTW', '3.3.10'),
+    ('PLUMED', '2.8.0'),
+]
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+]
+
+type = 'psmp'
+
+# regression test reports handful of failures,
+# we're assuming those are OK to ignore...
+ignore_regtest_fails = True
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb
new file mode 100644
index 00000000000..b2e72836ed6
--- /dev/null
+++ b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb
@@ -0,0 +1,39 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'CP2K'
+version = '9.1'
+
+homepage = 'https://www.cp2k.org/'
+description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular
+ simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different
+ methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and
+ classical pair and many-body potentials. """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['fedb4c684a98ad857cd49b69a3ae51a73f85a9c36e9cb63e3b02320c74454ce6']
+
+dependencies = [
+    ('Libint', '2.6.0', '-lmax-6-cp2k'),
+    ('libxc', '5.2.3'),
+    ('libxsmm', '1.17'),
+    ('FFTW', '3.3.10'),
+    ('PLUMED', '2.8.0'),
+]
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+]
+
+type = 'psmp'
+
+# regression test reports handful of failures,
+# we're assuming those are OK to ignore...
+ignore_regtest_fails = True
+
+moduleclass = 'chem'

From 68df9d6f35306cc5dd39e278b62e9337dc957ffe Mon Sep 17 00:00:00 2001
From: alin m elena <alinm.elena@gmail.com>
Date: Tue, 9 Aug 2022 13:17:43 +0100
Subject: [PATCH 023/601] deps for cp2k 2022a

---
 .../Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb    | 52 ++++++++++++++++
 .../l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb      | 27 +++++++++
 .../p/PLUMED/PLUMED-2.8.0-foss-2022a.eb       | 60 +++++++++++++++++++
 3 files changed, 139 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb
 create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb
new file mode 100644
index 00000000000..a992dd7921d
--- /dev/null
+++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb
@@ -0,0 +1,52 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'Libint'
+version = '2.6.0'
+local_lmax = 6
+# custom configuration, to be used as dependency for CP2K
+versionsuffix = '-lmax-%s-cp2k' % local_lmax
+
+homepage = 'https://github.com/evaleev/libint'
+description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
+ matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+source_urls = ['https://github.com/evaleev/libint/archive']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch',
+    'Libint-2.6.0_remove-test-eri.patch',
+]
+checksums = [
+    '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa',  # v2.6.0.tar.gz
+    # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch
+    'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab',
+    # Libint-2.6.0_remove-test-eri.patch
+    'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b',
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('GMP', '6.2.1'),
+    ('Boost', '1.79.0'),
+    ('Eigen', '3.4.0'),
+    ('Python', '3.10.4'),
+]
+
+# configure options as required by CP2K,
+# see Jenkinsfile in https://github.com/cp2k/libint-cp2k
+local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1)
+local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1)
+
+libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax
+libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am
+libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am
+libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am
+libint_compiler_configopts += '--enable-generic-code --disable-unrolling'
+
+with_fortran = True
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb
new file mode 100644
index 00000000000..9fbbdba6329
--- /dev/null
+++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'libxsmm'
+version = '1.17'
+
+homepage = 'https://github.com/hfp/libxsmm'
+description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications
+targeting Intel Architecture (x86)."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/hfp/libxsmm/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92']
+
+# install both static and dynamic version
+installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0']
+
+skipsteps = ['configure']
+maxparallel = 1
+
+sanity_check_paths = {
+    'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT],
+    'dirs': ['share']
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb
new file mode 100644
index 00000000000..8775e1beada
--- /dev/null
+++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb
@@ -0,0 +1,60 @@
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.8.0'
+
+homepage = 'https://www.plumed.org'
+description = """PLUMED is an open source library for free energy calculations in molecular systems which
+ works together with some of the most popular molecular dynamics engines. Free energy calculations can be
+ performed as a function of many order parameters with a particular  focus on biological problems, using
+ state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
+ The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': 'True'}
+
+source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
+sources = [SOURCE_TGZ]
+checksums = ['24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82']
+
+builddependencies = [
+    ('xxd', '8.2.4220'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('GSL', '2.7'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('Boost', '1.79.0'),
+]
+
+preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
+configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
+configopts += '--enable-boost_graph --enable-boost_serialization '
+configopts += '--enable-asmjit '
+prebuildopts = 'source sourceme.sh && '
+
+# make sure that ld.gold linker is used
+# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
+# (problem with intel build but maintain consistency between easyconfigs)
+buildopts = 'LD_RO="ld.gold -r -o"'
+
+# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
+preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
+
+sanity_check_paths = {
+    'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["python -c 'import plumed'"]
+
+modextrapaths = {
+    'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
+    'PLUMED_ROOT': 'lib/plumed',
+    'PYTHONPATH': 'lib/plumed/python',
+}
+
+moduleclass = 'chem'

From bdfc8f23c9c1687aacb973777d434dee64dd1de6 Mon Sep 17 00:00:00 2001
From: alin m elena <alinm.elena@gmail.com>
Date: Tue, 9 Aug 2022 13:36:16 +0100
Subject: [PATCH 024/601] needed by plumed

---
 .../x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb      | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..3aa02fbcfe1
--- /dev/null
+++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb
@@ -0,0 +1,39 @@
+# Last contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'MakeCp'
+
+name = 'xxd'
+version = '8.2.4220'
+
+homepage = 'https://www.vim.org'
+description = """xxd is part of the VIM package and this will only install xxd, not vim!
+xxd converts to/from hexdumps of binary files."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/vim/vim/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = [
+    '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604',  # v8.2.4220.tar.gz
+]
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+start_dir = 'src/xxd'
+
+files_to_copy = [
+    (['xxd'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/xxd'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"]
+
+moduleclass = 'tools'

From ece726e32922befb2d8c0df54407d3ce90486dd8 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 24 Aug 2022 08:25:44 +0200
Subject: [PATCH 025/601] adding easyconfigs: SLiM-4.0-GCC-11.2.0.eb and
 patches: SLiM-4.0_use_external_zlib_gsl.patch

---
 .../easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb |  48 ++++++
 .../SLiM/SLiM-4.0_use_external_zlib_gsl.patch | 161 ++++++++++++++++++
 2 files changed, 209 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb
 create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch

diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb
new file mode 100644
index 00000000000..a83b635112e
--- /dev/null
+++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb
@@ -0,0 +1,48 @@
+easyblock = 'CMakeMake'
+
+name = 'SLiM'
+version = '4.0'
+
+homepage = 'https://messerlab.org/slim'
+description = """SLiM is an evolutionary simulation framework that combines a powerful engine for population
+ genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/MesserLab/%(name)s/archive']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    '%(name)s-%(version)s_use_external_zlib_gsl.patch',
+]
+checksums = [
+    'd53ce9fc4ac00fa1dc3fc046ac21adb461ead46c1a0c54a72537a74873abf894',  # v4.0.tar.gz
+    '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755',  # SLiM-4.0_use_external_zlib_gsl.patch
+]
+
+builddependencies = [
+    ('CMake', '3.21.1'),
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('GSL', '2.7'),
+    ('Mesa', '21.1.7'),
+    ('libglvnd', '1.3.3'),
+    ('Qt5', '5.15.2'),
+]
+
+configopts = '-DBUILD_SLIMGUI=ON '
+
+sanity_check_paths = {
+    'files': ['bin/eidos', 'bin/slim'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "eidos -usage",
+    "eidos -testEidos",
+    "slim -usage",
+    "slim -testSLiM",
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch b/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch
new file mode 100644
index 00000000000..894f69dd4f3
--- /dev/null
+++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch
@@ -0,0 +1,161 @@
+commit 2ba4892b9327e5d21fdd712e178447d2ecd3665a
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Wed Aug 24 08:15:39 2022 +0200
+
+    Use external Zlib and GSL instead of internal ones.
+    And use correctly names zlib functions.
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 487c7bcd..0aae03ea 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -157,18 +157,20 @@ endif()
+ #endif()
+ 
+ # GSL 
+-set(TARGET_NAME gsl)
+-file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c)
+-set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg)
+-add_library(${TARGET_NAME} STATIC ${GSL_SOURCES})
+-target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES})
++# Use external GSL instead
++#set(TARGET_NAME gsl)
++#file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c)
++#set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg)
++#add_library(${TARGET_NAME} STATIC ${GSL_SOURCES})
++#target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES})
+ 
+ # ZLIB
+-set(TARGET_NAME eidos_zlib)
+-file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c)
+-set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib)
+-add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES})
+-target_include_directories(${TARGET_NAME} PUBLIC)
++# Use external Zlib instead
++#set(TARGET_NAME eidos_zlib)
++#file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c)
++#set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib)
++#add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES})
++#target_include_directories(${TARGET_NAME} PUBLIC)
+ 
+ # KASTORE
+ set(TARGET_NAME kastore)
+@@ -198,7 +200,7 @@ list(APPEND SLIM_SOURCES "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" ${PROJECT_SOU
+ 
+ add_executable(${TARGET_NAME} ${SLIM_SOURCES})
+ target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/eidos")
+-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables)
++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables)
+ if(WIN32)
+     set_source_files_properties(${SLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
+     set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
+@@ -211,7 +213,7 @@ set(TARGET_NAME eidos)
+ file(GLOB_RECURSE EIDOS_SOURCES  ${PROJECT_SOURCE_DIR}/eidos/*.cpp  ${PROJECT_SOURCE_DIR}/eidostool/*.cpp)
+ add_executable(${TARGET_NAME} ${EIDOS_SOURCES})
+ target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/eidos")
+-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables)
++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables)
+ if(WIN32)
+     set_source_files_properties(${EIDOS_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
+     set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
+@@ -244,15 +246,15 @@ set_target_properties( ${TARGET_NAME} PROPERTIES LINKER_LANGUAGE CXX)
+ target_compile_definitions( ${TARGET_NAME} PRIVATE EIDOSGUI=1 SLIMGUI=1)
+ target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore")
+ if(APPLE)
+-	target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib /usr/lib/libobjc.A.dylib )
++	target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z /usr/lib/libobjc.A.dylib )
+ else()
+     if(WIN32)
+         set_source_files_properties(${QTSLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
+         set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos SLiMgui PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
+         target_include_directories(${TARGET_NAME} BEFORE PUBLIC ${GNU_DIR})
+-        target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib gnu )
++        target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z gnu )
+     else()
+-	    target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib )
++	    target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z )
+     endif()
+ endif()
+ install(TARGETS ${TARGET_NAME} DESTINATION bin)
+diff --git a/eidos/eidos_functions.cpp b/eidos/eidos_functions.cpp
+index 4f52c763..ac9de199 100644
+--- a/eidos/eidos_functions.cpp
++++ b/eidos/eidos_functions.cpp
+@@ -55,11 +55,11 @@
+ 
+ #include "string.h"
+ 
+-#include "gsl_linalg.h"
+-#include "gsl_errno.h"
+-#include "gsl_cdf.h"
++#include <gsl/gsl_linalg.h>
++#include <gsl/gsl_errno.h>
++#include <gsl/gsl_cdf.h>
+ 
+-#include "../eidos_zlib/zlib.h"
++#include <zlib.h>
+ 
+ #include "eidos_globals.h"
+ #if EIDOS_ROBIN_HOOD_HASHING
+@@ -11475,7 +11475,7 @@ EidosValue_SP Eidos_ExecuteFunction_writeTempFile(const std::vector<EidosValue_S
+ 	if (do_compress)
+ 	{
+ 		// compression using zlib; very different from the no-compression case, unfortunately, because here we use C-based APIs
+-		gzFile gzf = z_gzdopen(fd, "wb");
++		gzFile gzf = gzdopen(fd, "wb");
+ 		
+ 		if (!gzf)
+ 		{
+diff --git a/eidos/eidos_globals.cpp b/eidos/eidos_globals.cpp
+index dc801c2f..95984159 100644
+--- a/eidos/eidos_globals.cpp
++++ b/eidos/eidos_globals.cpp
+@@ -65,13 +65,13 @@
+ #endif
+ 
+ // for Eidos_WelchTTest()
+-#include "gsl_cdf.h"
++#include <gsl/gsl_cdf.h>
+ 
+ // for Eidos_calc_sha_256()
+ #include <stdint.h>
+ 
+ // for _Eidos_FlushZipBuffer()
+-#include "../eidos_zlib/zlib.h"
++#include <zlib.h>
+ 
+ // for Eidos_ColorPaletteLookup()
+ #include "eidos_tinycolormap.h"
+@@ -1570,7 +1570,7 @@ bool _Eidos_FlushZipBuffer(const std::string &file_path, const std::string &outs
+ {
+ 	//std::cout << "_Eidos_FlushZipBuffer() called for " << file_path << std::endl;
+ 	
+-	gzFile gzf = z_gzopen(file_path.c_str(), "ab");
++	gzFile gzf = gzopen(file_path.c_str(), "ab");
+ 	
+ 	if (!gzf)
+ 		return false;
+@@ -1678,7 +1678,7 @@ void Eidos_WriteToFile(const std::string &p_file_path, std::vector<const std::st
+ 		{
+ 			// this code can handle both the append and the non-append case, but the append case may generate very low-quality
+ 			// compression (potentially even worse than the uncompressed data) due to having an excess of gzip headers
+-			gzFile gzf = z_gzopen(p_file_path.c_str(), p_append ? "ab" : "wb");
++			gzFile gzf = gzopen(p_file_path.c_str(), p_append ? "ab" : "wb");
+ 			
+ 			if (!gzf)
+ 				EIDOS_TERMINATION << "#ERROR (Eidos_WriteToFile): could not write to file at path " << p_file_path << "." << EidosTerminate(nullptr);
+diff --git a/eidos/eidos_rng.h b/eidos/eidos_rng.h
+index 313f75d7..7ab9db4d 100644
+--- a/eidos/eidos_rng.h
++++ b/eidos/eidos_rng.h
+@@ -29,8 +29,8 @@
+ 
+ // We have our own private copy of (parts of) the GSL library, so that we don't have link dependencies.
+ // See the _README file in the gsl directory for information on the local copy of the GSL included in this project.
+-#include "gsl_rng.h"
+-#include "gsl_randist.h"
++#include <gsl/gsl_rng.h>
++#include <gsl/gsl_randist.h>
+ 
+ #include <stdint.h>
+ #include <cmath>

From a16da39c4d4cb9eadb5a260d904c203abf7f835d Mon Sep 17 00:00:00 2001
From: casparl <caspar.vanleeuwen@surf.nl>
Date: Fri, 30 Sep 2022 19:08:39 +0200
Subject: [PATCH 026/601] adding easyconfigs:
 jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb and patches:
 jupyter-resource-usage-0.6.2_fix_update_cpu.patch

---
 ...ter-resource-usage-0.6.2-GCCcore-10.3.0.eb | 69 +++++++++++++++++++
 ...-resource-usage-0.6.2_fix_update_cpu.patch | 16 +++++
 2 files changed, 85 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb
 create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch

diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb
new file mode 100644
index 00000000000..37c5915ff8e
--- /dev/null
+++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb
@@ -0,0 +1,69 @@
+easyblock = 'PythonBundle'
+
+name = 'jupyter-resource-usage'
+version = '0.6.2'
+
+homepage = 'https://github.com/jupyter-server/jupyter-resource-usage'
+description = """Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+
+builddependencies = [
+    ('binutils', '2.36.1'),
+]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('IPython', '7.25.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('websocket-client', '1.4.1', {
+        'modulename': 'websocket',
+        'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'],
+    }),
+    ('sniffio', '1.3.0', {
+        'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'],
+    }),
+    ('anyio', '3.6.1', {
+        'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'],
+    }),
+    ('requests-unixsocket', '0.3.0', {
+        'checksums': ['28304283ea9357d45fff58ad5b11e47708cfbf5806817aa59b2a363228ee971e'],
+    }),
+    ('jupyter_server', '1.11.1', {
+        'checksums': ['ab7ab1cc38512f15026cbcbb96300fb46ec8b24aa162263d9edd00e0a749b1e8'],
+    }),
+    (name, version, {
+        'patches': [
+            'jupyter-resource-usage-0.6.1_compatibility.patch',
+            'jupyter-resource-usage-0.6.2_fix_update_cpu.patch',
+        ],
+        'checksums': [
+            '735acfe9516c68d1f50c25f74b236075da2adde49f734b24f6d2578ab9aa8d0c',  # jupyter-resource-usage-0.6.2.tar.gz
+            # jupyter-resource-usage-0.6.1_compatibility.patch
+            'b030065413bac04bd40088cd92be98bac3e92d68189d03d338986444af3953f4',
+            # jupyter-resource-usage-0.6.2_fix_update_cpu.patch
+            'e2d2ea15211c90faebb57c1170a105f94fe0fd28055a69969dd53dad9ff7f990',
+        ],
+    }),
+]
+
+# Add the notebook extension to the search path for jupyter notebooks
+modextrapaths = {
+    'JUPYTER_PATH': 'share/jupyter/',
+}
+
+sanity_check_paths = {
+    'dirs': [
+        'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage',
+        'lib/python%(pyshortver)s/site-packages/jupyter_server'
+    ],
+    'files': ['bin/jupyter-server'],
+}
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch
new file mode 100644
index 00000000000..181500591a5
--- /dev/null
+++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch
@@ -0,0 +1,16 @@
+# Author: Caspar van Leeuwen, SURF
+# If the CPU was idle (i.e. cpuPercent=0), the display showing CPU usage wouldn't update,
+# because of a faulty logic. This patch fixes that.
+# See https://github.com/jupyter-server/jupyter-resource-usage/pull/147
+diff -Nru jupyter-resource-usage-0.6.2.orig/jupyter_resource_usage/static/main.js jupyter-resource-usage-0.6.2/jupyter_resource_usage/static/main.js
+--- jupyter-resource-usage-0.6.2.orig/jupyter_resource_usage/static/main.js	2022-09-30 19:02:36.892711996 +0200
++++ jupyter-resource-usage-0.6.2/jupyter_resource_usage/static/main.js	2022-09-30 19:02:59.994787990 +0200
+@@ -74,7 +74,7 @@
+ 
+                 // Handle CPU display
+                 var cpuPercent = data['cpu_percent'];
+-                if (cpuPercent) {
++                if (cpuPercent !== undefined) {
+                     // Remove hide CSS class if the metrics API gives us a CPU percent to display
+                     $('#jupyter-resource-usage-display-cpu').removeClass('jupyter-resource-usage-hide');
+                     var maxCpu = data['cpu_count'];

From 69161e475b54b98514eb45ccef68b95c1e418b62 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 21 Oct 2022 19:10:57 +0200
Subject: [PATCH 027/601] adding easyconfigs: Scalene-1.5.13-GCCcore-11.2.0.eb

---
 .../Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb  | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb
new file mode 100644
index 00000000000..838f20f9ff1
--- /dev/null
+++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'Scalene'
+version = '1.5.13'
+
+homepage = 'https://github.com/plasma-umass/scalene'
+description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things
+that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while
+delivering far more detailed information."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+dependencies = [
+    ('Python', '3.9.6'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('cloudpickle', '2.2.0', {
+        'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'],
+    }),
+    ('pynvml', '11.4.1', {
+        'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'],
+    }),
+    ('commonmark', '0.9.1', {
+        'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'],
+    }),
+    ('rich', '12.6.0', {
+        'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
+        'checksums': ['0077d517249cfa6ad0953d85c9656bdaca57b863159bbb78969987d9bdbb539c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/scalene'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["scalene --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 80b2ba06f7d79853259febdd9c292a511f0b7b93 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 24 Oct 2022 16:44:32 +0100
Subject: [PATCH 028/601] adding easyconfigs: MoviePy-1.0.3-foss-2021b.eb

---
 .../m/MoviePy/MoviePy-1.0.3-foss-2021b.eb     | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb

diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
new file mode 100644
index 00000000000..dbe91a2e7ff
--- /dev/null
+++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
@@ -0,0 +1,42 @@
+# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
+# Updated to foss 2021b: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'PythonBundle'
+
+name = 'MoviePy'
+version = '1.0.3'
+
+homepage = "https://zulko.github.io/moviepy/"
+description = """MoviePy (full documentation) is a Python library for video editing: cutting, concatenations,
+ title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+dependencies = [
+    ('FFmpeg', '4.3.2'),
+    ('Python', '3.9.6'),
+    ('Pillow', '8.3.2'),
+    ('SciPy-bundle', '2021.10'),
+    ('tqdm', '4.62.3'),
+    ('imageio', '2.13.5'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('imageio-ffmpeg', '0.4.7', {
+        'checksums': ['7a08838f97f363e37ca41821b864fd3fdc99ab1fe2421040c78eb5f56a9e723e'],
+    }),
+    ('proglog', '0.1.10', {
+        'checksums': ['658c28c9c82e4caeb2f25f488fff9ceace22f8d69b15d0c1c86d64275e4ddab4'],
+    }),
+    (name, version, {
+        'source_tmpl': 'moviepy-%(version)s.tar.gz',
+        'patches': ['moviepy-1.0.3-setup.py.patch'],
+        'checksums': [('2884e35d1788077db3ff89e763c5ba7bfddbd7ae9108c9bc809e7ba58fa433f5'),
+                      ('beca82ff8dfbc9cd0b97296f310de3ddfc43e2e49344a32375d4438485c3f3df')],
+    }),
+]
+
+moduleclass = 'tools'

From 49d6e098fc35372a98d9421f094843235bced23b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 25 Oct 2022 10:59:31 +0200
Subject: [PATCH 029/601] binutils

---
 .../easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb    | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb
index 838f20f9ff1..5f49d35f2d6 100644
--- a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb
@@ -10,6 +10,10 @@ delivering far more detailed information."""
 
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
+builddependencies = [
+    ('binutils', '2.37'),
+]
+
 dependencies = [
     ('Python', '3.9.6'),
 ]

From e93413cf51ff51a78519259e7e80f95d061376d8 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Sun, 20 Nov 2022 20:12:23 +0000
Subject: [PATCH 030/601] sanity_check_paths added as a check

---
 easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
index dbe91a2e7ff..0526cbdc186 100644
--- a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
+++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
@@ -39,4 +39,9 @@ exts_list = [
     }),
 ]
 
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
 moduleclass = 'tools'

From 84856245897c83e988e80b691273deb21e18ad65 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <a.ocais@fz-juelich.de>
Date: Tue, 22 Nov 2022 10:50:35 +0000
Subject: [PATCH 031/601] adding easyconfigs: Clang-15.0.5-GCCcore-11.3.0.eb

---
 .../c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb    | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..2e95433ea04
--- /dev/null
+++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
@@ -0,0 +1,51 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans
+# Authors:: Dmitri Gribenko <gribozavr@gmail.com>
+# Authors:: Ward Poelmans <wpoely86@gmail.com>
+# License:: GPLv2 or later, MIT, three-clause BSD.
+# $Id$
+##
+
+name = 'Clang'
+version = '15.0.5'
+
+homepage = 'https://clang.llvm.org/'
+description = """C, C++, Objective-C compiler, based on LLVM.  Does not
+ include C++ standard library -- use libstdc++ from GCC."""
+
+# Clang also depends on libstdc++ during runtime, but this dependency is
+# already specified as the toolchain.
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"]
+sources = [
+    'llvm-project-%(version)s.src.tar.xz',
+]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('Perl', '5.34.1'),
+    ('elfutils', '0.187'),
+]
+dependencies = [
+    # since Clang is a compiler, binutils is a runtime dependency too
+    ('binutils', '2.38'),
+    ('hwloc', '2.7.1'),
+    ('libxml2', '2.9.13'),
+    ('ncurses', '6.3'),
+    ('GMP', '6.2.1'),
+    ('Z3', '4.10.2'),
+    ('Python', '3.10.4'),
+]
+
+assertions = True
+enable_rtti = True
+python_bindings = True
+skip_all_tests = True
+
+llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi']
+llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang']
+
+moduleclass = 'compiler'

From ef035ef6bf0fdcd102eff3a2810ad4a8dd1e2ba4 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 22 Nov 2022 22:49:21 +0100
Subject: [PATCH 032/601] Update Clang-15.0.5-GCCcore-11.3.0.eb

---
 easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
index 2e95433ea04..06fb908fe9f 100644
--- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
@@ -23,6 +23,7 @@ source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%
 sources = [
     'llvm-project-%(version)s.src.tar.xz',
 ]
+checksums = ['9c4278a6b8884eb7f4ae7dfe3c8e5445019824885e47cfdf1392563c47316fd6']
 
 builddependencies = [
     ('CMake', '3.23.1'),

From 1593e419b60dc6f7f4e58b3c1f0c44f7f6ac6d9b Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 25 Nov 2022 11:01:15 +0100
Subject: [PATCH 033/601] Disable RTTI when using flang project

---
 .../easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb     | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
index 06fb908fe9f..f70ecde5774 100644
--- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
@@ -41,8 +41,13 @@ dependencies = [
     ('Python', '3.10.4'),
 ]
 
+# enabling RTTI makes the flang compiler need to link to libc++ so instead of
+#   flang-new -flang-experimental-exec -fopenmp hello_openmp.f90
+# you would need
+#   flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++
+enable_rtti = False
+
 assertions = True
-enable_rtti = True
 python_bindings = True
 skip_all_tests = True
 

From bf68567e0d07953ce50043a911f768c59b455b62 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 29 Nov 2022 11:52:13 +0100
Subject: [PATCH 034/601] adding easyconfigs: Simple-DFTD3-0.7.0-foss-2022a.eb,
 mstore-0.2.0-GCCcore-11.3.0.eb, mctc-lib-0.3.1-GCCcore-11.3.0.eb,
 TOML-Fortran-0.3.1-GCC-11.3.0.eb

---
 .../mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb | 33 ++++++++++++++++
 .../m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb   | 34 +++++++++++++++++
 .../Simple-DFTD3-0.7.0-foss-2022a.eb          | 38 +++++++++++++++++++
 .../TOML-Fortran-0.3.1-GCC-11.3.0.eb          | 24 ++++++++++++
 4 files changed, 129 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..c2fa48c5c80
--- /dev/null
+++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'CMakeMake'
+
+name = 'mctc-lib'
+version = '0.3.1'
+
+homepage = 'https://grimme-lab.github.io/mctc-lib'
+description = """Common tool chain for working with molecular structure data in various
+applications. This library provides a unified way to perform operations on
+molecular structure data, like reading and writing to common geometry file
+formats."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'grimme-lab'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=1'
+
+sanity_check_paths = {
+    'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT],
+    'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'],
+}
+
+sanity_check_commands = ["mctc-convert --help"]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..ab7413786e6
--- /dev/null
+++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'mstore'
+version = '0.2.0'
+
+homepage = 'https://github.com/grimme-lab/mstore'
+description = """Molecular structure store for testing"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'grimme-lab'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('mctc-lib', '0.3.1'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=1'
+
+sanity_check_paths = {
+    'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT],
+    'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'],
+}
+
+sanity_check_commands = ["mstore-info --help"]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
new file mode 100644
index 00000000000..f138326bdda
--- /dev/null
+++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'Simple-DFTD3'
+version = '0.7.0'
+
+homepage = 'https://dftd3.readthedocs.io'
+description = """Reimplementation of the D3 dispersion correction. The s-dftd3 project aims to
+provide a user-friendly and uniform interface to the D3 dispersion model and
+for the calculation of DFT-D3 dispersion corrections."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': False, 'openmp': True, 'pic': True}
+
+github_account = 'dftd3'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['19400a176eb4dcee7b89181a5a5f0033fe6b05c52821e54896a98448761d003a']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('mctc-lib', '0.3.1'),
+    ('mstore', '0.2.0'),
+    ('TOML-Fortran', '0.3.1'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=1 -DWITH_BLAS=1 -DWITH_OpenMP=1'
+
+sanity_check_paths = {
+    'files': ['bin/s-dftd3', 'lib/libs-dftd3.%s' % SHLIB_EXT, 'include/dftd3.h', 'include/s-dftd3.h'],
+    'dirs': ['include/s-dftd3', 'lib/cmake', 'lib/pkgconfig'],
+}
+
+sanity_check_commands = ["s-dftd3 --help"]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb
new file mode 100644
index 00000000000..99fc626c682
--- /dev/null
+++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'CMakeMake'
+
+name = 'TOML-Fortran'
+version = '0.3.1'
+
+homepage = 'https://github.com/toml-f/toml-f'
+description = 'TOML parser for Fortran projects'
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['7586f0be7dc88dddba4d4e42059b84baa2688a2784bdc1d1f37112ab3edb88e1']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libtoml-f.a'],
+    'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'],
+}
+
+moduleclass = 'tools'

From bcbd77ae885715ccb23a87df853286a26d98e532 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 29 Nov 2022 13:48:41 +0100
Subject: [PATCH 035/601] add build dependency on binutils to mstore and
 mctc-lib

---
 .../easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb      | 1 +
 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb    | 1 +
 2 files changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb
index c2fa48c5c80..026ff55fa14 100644
--- a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb
@@ -18,6 +18,7 @@ sources = ['v%(version)s.tar.gz']
 checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083']
 
 builddependencies = [
+    ('binutils', '2.38'),
     ('CMake', '3.23.1'),
 ]
 
diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
index ab7413786e6..8ddbf0c4fc0 100644
--- a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
@@ -15,6 +15,7 @@ sources = ['v%(version)s.tar.gz']
 checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d']
 
 builddependencies = [
+    ('binutils', '2.38'),
     ('CMake', '3.23.1'),
 ]
 

From dd4cbe8810d95c17642d6416639aba75f0ec7540 Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Mon, 5 Dec 2022 18:27:37 +0000
Subject: [PATCH 036/601] adding easyconfigs: XGBoost-1.7.1-foss-2022a.eb

---
 .../x/XGBoost/XGBoost-1.7.1-foss-2022a.eb     | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb
new file mode 100644
index 00000000000..36425089ffc
--- /dev/null
+++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'XGBoost'
+version = '1.7.1'
+
+homepage = 'https://github.com/dmlc/xgboost'
+description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient,
+ flexible and portable."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['bb302c5c33e14bab94603940987940f29203ecb8767a7a719daf579fbfaace64']
+
+builddependencies = [('CMake', '3.23.1')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+# use the parallel parameter from EB instead of total procs in the system
+preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&"
+
+moduleclass = 'lib'

From 7e7310cc2e356865cd2c5f8502dfb7f5f521c728 Mon Sep 17 00:00:00 2001
From: Alexandre Strube <surak@surak.eti.br>
Date: Wed, 7 Dec 2022 17:46:30 +0000
Subject: [PATCH 037/601] adding easyconfigs:
 PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb

---
 ...0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..d75c64e868c
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb
@@ -0,0 +1,60 @@
+easyblock = 'PythonBundle'
+
+name = 'PyTorch-Geometric'
+version = '2.1.0'
+local_pytorchver = '1.12.0'
+versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pytorchver
+
+homepage = 'https://github.com/rusty1s/pytorch_geometric'
+description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('PyTorch', local_pytorchver, '-CUDA-%(cudaver)s'),
+    ('scikit-learn', '1.1.2'),
+    ('scikit-image', '0.19.3'),
+    ('numba', '0.56.4', '-CUDA-%(cudaver)s'),
+    ('h5py', '3.7.0'),
+    ('tqdm', '4.64.0'),
+    ('RDFlib', '6.2.0'),
+    ('ASE', '3.22.1'),
+    ('YACS', '0.1.8'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('googledrivedownloader', '0.4', {
+        'modulename': 'google_drive_downloader',
+        'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'],
+    }),
+    ('plyfile', '0.7.4', {
+        'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'],
+    }),
+    ('torch_scatter', version, {
+        'checksums': ['3a7124c2a033552febbdc72407f7d4d8cb6dce465720e84ab831512e81c1d208'],
+    }),
+    ('torch_sparse', '0.6.15', {
+        'checksums': ['3a741ae8a7cc19247a44de549fa4d593c4257b5f741e1eb5110b712a14209dd9'],
+    }),
+    ('torch_cluster', '1.6.0', {
+        'checksums': ['249c1bd8c33a887b22bf569a59d0868545804032123594dd8c76ba1885859c39'],
+    }),
+    ('torch_spline_conv', '1.2.1', {
+        'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'],
+    }),
+    ('python-louvain', '0.16', {
+        'modulename': 'community.community_louvain',
+        'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'],
+    }),
+    ('torch_geometric', version, {
+        'checksums': ['72653deca925885e4d613eb5c72268bb9710325d9c717516922499fbe1197079'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 4b45c4c5bd4efbbe2ecd9a6047f9a32015bfd1f5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 8 Dec 2022 12:28:40 +0100
Subject: [PATCH 038/601] {geo}[foss/2022.10] WRF v4.4.1, tcsh v6.24.05, time
 v1.9

---
 .../t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb     | 45 ++++++++++++++++
 .../t/time/time-1.9-GCCcore-12.2.0.eb         | 27 ++++++++++
 .../w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb     | 51 +++++++++++++++++++
 3 files changed, 123 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb

diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..5874f3e8c14
--- /dev/null
+++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb
@@ -0,0 +1,45 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit
+# Authors::   Valentin Plugaru <valentin.plugaru@gmail.com>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html
+##
+easyblock = 'ConfigureMake'
+
+name = 'tcsh'
+version = '6.24.05'
+
+homepage = 'https://www.tcsh.org'
+description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh).
+ It is a command language interpreter usable both as an interactive login shell and a shell script command
+ processor. It includes a command-line editor, programmable word completion, spelling correction, a history
+ mechanism, job control and a C-like syntax."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [
+    'https://astron.com/pub/%(namelower)s',
+    'https://astron.com/pub/%(namelower)s/old',
+    'ftp://ftp.astron.com/pub/%(namelower)s',
+    'ftp://ftp.astron.com/pub/%(namelower)s/old',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3d1ff94787859b5a4063400470251618f76bc24f8041ba7ef2c2753f782c296c']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [('ncurses', '6.3')]
+
+postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"]
+
+sanity_check_paths = {
+    'files': ["bin/tcsh", "bin/csh"],
+    'dirs': []
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..e241a9de1bc
--- /dev/null
+++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'time'
+version = '1.9'
+
+homepage = 'https://www.gnu.org/software/time/'
+description = """The `time' command runs another program, then displays information about the resources used by that
+ program, collected by the system while the program was running."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e']
+
+builddependencies = [('binutils', '2.39')]
+
+postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"]
+
+sanity_check_paths = {
+    'files': ['bin/gtime', 'bin/%(name)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["time echo test"]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb
new file mode 100644
index 00000000000..95e02318341
--- /dev/null
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb
@@ -0,0 +1,51 @@
+name = 'WRF'
+version = '4.4.1'
+buildtype = 'dmpar'
+versionsuffix = '-%s' % buildtype
+
+homepage = 'https://www.wrf-model.org'
+description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale
+ numerical weather prediction system designed to serve both operational forecasting and atmospheric
+ research needs."""
+
+toolchain = {'name': 'foss', 'version': '2022.10'}
+toolchainopts = {'opt': False}  # don't use agressive optimization, stick to -O2
+
+source_urls = ['https://github.com/wrf-model/WRF/archive/']
+# sources = ['v%(version)s.tar.gz']
+sources = [{
+    'filename': 'v%(version)s.tar.gz',
+    'git_config': {
+        'url': 'https://github.com/wrf-model',
+        'repo_name': 'WRF',
+        'tag': 'v%(version)s',
+        'clone_into': 'WRF-%(version)s',
+        'recursive': True,
+    },
+}]
+patches = [
+    'WRF-4.4_netCDF-Fortran_separate_path.patch',
+]
+checksums = [
+    None,  # v4.4.1.tar.gz
+    '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff',  # WRF-4.4_netCDF-Fortran_separate_path.patch
+]
+
+# csh is used by WRF install scripts
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('tcsh', '6.24.05'),
+    ('time', '1.9'),
+    ('Perl', '5.36.0'),
+]
+
+dependencies = [
+    ('JasPer', '4.0.0'),
+    ('netCDF', '4.9.0'),
+    ('netCDF-Fortran', '4.6.0'),
+]
+
+# limit parallel build to 20
+maxparallel = 20
+
+moduleclass = 'geo'

From 4f77406b81a728a791e17257e3b15021fcf005f6 Mon Sep 17 00:00:00 2001
From: "e.dilorenzo" <e.dilorenzo@enginsoft.com>
Date: Wed, 21 Dec 2022 18:19:12 +0100
Subject: [PATCH 039/601] adding easyconfigs:
 libgcrypt-1.10.1-GCCcore-11.3.0.eb

---
 .../libgcrypt-1.10.1-GCCcore-11.3.0.eb        | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..36bfe330597
--- /dev/null
+++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'libgcrypt'
+version = '1.10.1'
+
+homepage = 'https://gnupg.org/related_software/libgcrypt/index.html'
+description = """Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['ef14ae546b0084cd84259f61a55e07a38c3b53afc0f546bffcef2f01baffe9de']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [('libgpg-error', '1.46')]
+
+sanity_check_paths = {
+    'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT],
+    'dirs': ['share']
+}
+
+moduleclass = 'system'

From d8e998c4f31dd8c9fbc6d715d9bae135b72ad033 Mon Sep 17 00:00:00 2001
From: "e.dilorenzo" <e.dilorenzo@enginsoft.com>
Date: Fri, 23 Dec 2022 12:42:27 +0100
Subject: [PATCH 040/601] adding easyconfigs:
 Cantera-2.6.0-foss-2022a-Python-3.10.4.eb

---
 .../Cantera-2.6.0-foss-2022a-Python-3.10.4.eb | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb

diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
new file mode 100644
index 00000000000..607648036f0
--- /dev/null
+++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
@@ -0,0 +1,50 @@
+easyblock = 'SCons'
+
+name = 'Cantera'
+version = '2.6.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/Cantera/cantera'
+description = """Chemical kinetics, thermodynamics, and transport tool suite"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'strict': True}
+
+source_urls = ['https://github.com/Cantera/cantera/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['7273622ea76a53373cee820f939613b15eea3dd83db6e1b127c5ed043f77dc5b']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Boost', '1.79.0'),
+    ('SUNDIALS', '6.3.0'),
+    ('yaml-cpp', '0.7.0'),
+    ('ruamel.yaml', '0.17.21'),
+]
+builddependencies = [
+    ('SCons', '4.4.0'),
+    ('Eigen', '3.4.0'),
+    ('fmt', '9.1.0'),
+    ('googletest', '1.11.0'),
+]
+
+local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" '
+#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR '
+#local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib'
+#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib'
+buildopts = 'build ' + local_common_opts
+# tests hang, so disable them for now
+# runtest = 'test ' + local_common_opts
+installopts = 'install ' + local_common_opts
+prefix_arg = 'prefix='
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+sanity_check_paths = {
+    'files': ['bin/ck2cti'],
+    'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [('python', "-c 'import cantera'")]
+
+moduleclass = 'chem'

From 5dc16b7067cd06de87114439dbfc171600d35897 Mon Sep 17 00:00:00 2001
From: iotaka <edoardo.dilorenzo@gmail.com>
Date: Wed, 28 Dec 2022 14:23:46 +0100
Subject: [PATCH 041/601] Update Cantera-2.6.0-foss-2022a-Python-3.10.4.eb

---
 .../c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
index 607648036f0..0f2cbfc44ef 100644
--- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
+++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
@@ -29,9 +29,9 @@ builddependencies = [
 ]
 
 local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" '
-#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR '
-#local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib'
-#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib'
+# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR '
+# local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib'
+# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib'
 buildopts = 'build ' + local_common_opts
 # tests hang, so disable them for now
 # runtest = 'test ' + local_common_opts

From 33cc1ff434e303cb9cd0de80b987b312c6796f4f Mon Sep 17 00:00:00 2001
From: iotaka <edoardo.dilorenzo@gmail.com>
Date: Wed, 28 Dec 2022 14:45:37 +0100
Subject: [PATCH 042/601] Update Cantera-2.6.0-foss-2022a-Python-3.10.4.eb

---
 .../c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb          | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
index 0f2cbfc44ef..bb14dcff6b1 100644
--- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
+++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
@@ -2,7 +2,6 @@ easyblock = 'SCons'
 
 name = 'Cantera'
 version = '2.6.0'
-versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/Cantera/cantera'
 description = """Chemical kinetics, thermodynamics, and transport tool suite"""

From dc70dfb27367d78d752a1313cec4de67797dcef8 Mon Sep 17 00:00:00 2001
From: iotaka <edoardo.dilorenzo@gmail.com>
Date: Wed, 28 Dec 2022 15:12:36 +0100
Subject: [PATCH 043/601] Rename Cantera-2.6.0-foss-2022a-Python-3.10.4.eb to
 Cantera-2.6.0-foss-2022a.eb

---
 ....0-foss-2022a-Python-3.10.4.eb => Cantera-2.6.0-foss-2022a.eb} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/c/Cantera/{Cantera-2.6.0-foss-2022a-Python-3.10.4.eb => Cantera-2.6.0-foss-2022a.eb} (100%)

diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb
similarity index 100%
rename from easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb
rename to easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb

From 5c71bb87a57f8a757d9467ac15e6f25b16b34c62 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Wed, 4 Jan 2023 18:38:15 +0100
Subject: [PATCH 044/601] Fixed raven using highest version on Python found

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index ff53344aa8a..ecfc1e3b520 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -18,7 +18,9 @@ builddependencies = [
 ]
 
 preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && "
-configopts = ['-DRAVEN_BUILD_EXE=1 -G Ninja ']
+configopts = '-DRAVEN_BUILD_EXE=1 -G Ninja '
+configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
+
 
 dependencies = [
     ('Python', '3.9.6'),

From 3a4edaa2df44dc4cc6a8539fa1bf98614ec0b7de Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Thu, 5 Jan 2023 16:48:30 +0100
Subject: [PATCH 045/601] Modified setup.py according to the recommendation

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index ecfc1e3b520..502affd4f48 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -40,6 +40,8 @@ exts_list = [
         'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'],
         'sources': ['%(version)s.tar.gz'],
         'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'],
+        'preinstallopts': 'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \
+            "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION"\]|\' setup.py && '
     }),
 ]
 

From 4e565b99b1abd518221f48a510010f156a887525 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Wed, 11 Jan 2023 17:21:11 +0100
Subject: [PATCH 046/601] Added Python3_EXECUTABLE argument to ravenpy

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index 502affd4f48..ecf094af5d5 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -41,7 +41,8 @@ exts_list = [
         'sources': ['%(version)s.tar.gz'],
         'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'],
         'preinstallopts': 'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \
-            "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION"\]|\' setup.py && '
+            "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",\
+            "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|\' setup.py && '
     }),
 ]
 

From 7df7a7dd70e74d9d5c1dae57426de4eced3cee66 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 18 Jan 2023 15:51:06 +0100
Subject: [PATCH 047/601] build Simple-DFTD3 with CMakeNinja and run tests

---
 .../s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb    | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
index f138326bdda..1cedb90bf3c 100644
--- a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
@@ -1,4 +1,4 @@
-easyblock = 'CMakeMake'
+easyblock = 'CMakeNinja'
 
 name = 'Simple-DFTD3'
 version = '0.7.0'
@@ -18,6 +18,7 @@ checksums = ['19400a176eb4dcee7b89181a5a5f0033fe6b05c52821e54896a98448761d003a']
 
 builddependencies = [
     ('CMake', '3.23.1'),
+    ('Ninja', '1.10.2'),
 ]
 
 dependencies = [
@@ -26,7 +27,12 @@ dependencies = [
     ('TOML-Fortran', '0.3.1'),
 ]
 
-configopts = '-DBUILD_SHARED_LIBS=1 -DWITH_BLAS=1 -DWITH_OpenMP=1'
+build_shared_libs = True
+
+configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1'
+
+test_cmd = 'ctest'
+runtest = ''
 
 sanity_check_paths = {
     'files': ['bin/s-dftd3', 'lib/libs-dftd3.%s' % SHLIB_EXT, 'include/dftd3.h', 'include/s-dftd3.h'],

From d7f1d99b8e67affed19b6e87c2a079c7ef173346 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 18 Jan 2023 15:52:27 +0100
Subject: [PATCH 048/601] add author contributions to Simple-DFTD3

---
 .../s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb            | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
index 1cedb90bf3c..4d92d2d0cde 100644
--- a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
@@ -1,3 +1,6 @@
+# A. Domingo (Vrije Universiteit Brussel)
+# J. Sassmannshausen (Imperial College London/UK)
+
 easyblock = 'CMakeNinja'
 
 name = 'Simple-DFTD3'

From a68e55ca6f0a078485b5edfb144cb5ae380f11aa Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 19 Jan 2023 10:23:28 +0100
Subject: [PATCH 049/601] adding easyconfigs: PyTorch-1.12.1-foss-2021b.eb

---
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b.eb    | 132 ++++++++++++++++++
 1 file changed, 132 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
new file mode 100644
index 00000000000..b4e4f83ca06
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
@@ -0,0 +1,132 @@
+name = 'PyTorch'
+version = '1.12.1'
+
+homepage = 'https://pytorch.org/'
+description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration.
+PyTorch is a deep learning framework that puts Python first."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = [GITHUB_RELEASE]
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+
+patches = [
+    'PyTorch-1.7.0_avoid-nan-in-test-torch.patch',
+    'PyTorch-1.7.0_disable-dev-shm-test.patch',
+    'PyTorch-1.10.0_fix-kineto-crash.patch',
+    'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch',
+    'PyTorch-1.10.0_fix-test-model_dump.patch',
+    'PyTorch-1.10.0_fix-vsx-vector-functions.patch',
+    'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch',
+    'PyTorch-1.11.0_fix-fsdp-fp16-test.patch',
+    'PyTorch-1.11.0_fix-test_utils.patch',
+    'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch',
+    'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
+    'PyTorch-1.11.0_install-vsx-vec-headers.patch',
+    'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
+    'PyTorch-1.12.1_fix-skip-decorators.patch',
+    'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
+    'PyTorch-1.12.1_fix-test_wishart_log_prob.patch',
+    'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch',
+    'PyTorch-1.12.1_fix-TestTorch.test_to.patch',
+    'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch',
+    'PyTorch-1.12.1_fix-vsx-vector-funcs.patch',
+    'PyTorch-1.12.1_fix-vsx-loadu.patch',
+    'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch',
+    'PyTorch-1.12.1_increase-tolerance-test_ops.patch',
+    'PyTorch-1.12.1_no-cuda-stubs-rpath.patch',
+    'PyTorch-1.12.1_python-3.10-annotation-fix.patch',
+    'PyTorch-1.12.1_python-3.10-compat.patch',
+    'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch',
+    'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
+    'PyTorch-1.12.1_skip-failing-grad-test.patch',
+    'PyTorch-1.12.1_skip-test_round_robin.patch',
+]
+checksums = [
+    '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
+    'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18',  # PyTorch-1.7.0_avoid-nan-in-test-torch.patch
+    '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a',  # PyTorch-1.7.0_disable-dev-shm-test.patch
+    # PyTorch-1.10.0_fix-kineto-crash.patch
+    'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb',
+    # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch
+    '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707',
+    # PyTorch-1.10.0_fix-test-model_dump.patch
+    '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557',
+    # PyTorch-1.10.0_fix-vsx-vector-functions.patch
+    '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312',
+    # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch
+    '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2',
+    'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13',  # PyTorch-1.11.0_fix-fsdp-fp16-test.patch
+    '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861',  # PyTorch-1.11.0_fix-test_utils.patch
+    # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch
+    '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953',
+    # PyTorch-1.11.0_increase-distributed-test-timeout.patch
+    '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f',
+    'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
+    # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
+    'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab',
+    'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c',  # PyTorch-1.12.1_fix-skip-decorators.patch
+    # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch
+    '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83',
+    # PyTorch-1.12.1_fix-test_wishart_log_prob.patch
+    'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45',
+    # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch
+    '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2',
+    '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535',  # PyTorch-1.12.1_fix-TestTorch.test_to.patch
+    # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch
+    '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d',
+    'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2',  # PyTorch-1.12.1_fix-vsx-vector-funcs.patch
+    '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2',  # PyTorch-1.12.1_fix-vsx-loadu.patch
+    # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch
+    '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695',
+    # PyTorch-1.12.1_increase-tolerance-test_ops.patch
+    '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb',
+    '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6',  # PyTorch-1.12.1_no-cuda-stubs-rpath.patch
+    # PyTorch-1.12.1_python-3.10-annotation-fix.patch
+    '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7',
+    '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67',  # PyTorch-1.12.1_python-3.10-compat.patch
+    # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch
+    'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d',
+    # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch
+    'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39',
+    '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
+    # PyTorch-1.12.1_skip-test_round_robin.patch
+    '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349',
+]
+
+osdependencies = [OS_PKG_IBVERBS_DEV]
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+    ('hypothesis', '6.14.6'),
+]
+
+dependencies = [
+    ('Ninja', '1.10.2'),  # Required for JIT compilation of C++ extensions
+    ('Python', '3.9.6'),
+    ('protobuf', '3.17.3'),
+    ('protobuf-python', '3.17.3'),
+    ('pybind11', '2.7.1'),
+    ('SciPy-bundle', '2021.10'),
+    ('typing-extensions', '3.10.0.2'),
+    ('PyYAML', '5.4.1'),
+    ('MPFR', '4.1.0'),
+    ('GMP', '6.2.1'),
+    ('numactl', '2.0.14'),
+    ('FFmpeg', '4.3.2'),
+    ('Pillow', '8.3.2'),
+    ('expecttest', '0.1.3'),
+]
+
+excluded_tests = {
+    '': [
+        # This test seems to take too long on NVIDIA Ampere at least.
+        'distributed/test_distributed_spawn',
+    ]
+}
+
+runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error  --verbose %(excluded_tests)s'
+
+tests = ['PyTorch-check-cpp-extension.py']
+
+moduleclass = 'ai'

From 1d1afb493e82b907df64093e36d460ca2e5f4664 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 24 Jan 2023 13:17:22 +0100
Subject: [PATCH 050/601] Don't build the python bindings

---
 easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
index f70ecde5774..28274b11f14 100644
--- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
@@ -38,7 +38,8 @@ dependencies = [
     ('ncurses', '6.3'),
     ('GMP', '6.2.1'),
     ('Z3', '4.10.2'),
-    ('Python', '3.10.4'),
+    # Including Python bindings would require this dep
+    # ('Python', '3.10.4'),
 ]
 
 # enabling RTTI makes the flang compiler need to link to libc++ so instead of
@@ -48,7 +49,7 @@ dependencies = [
 enable_rtti = False
 
 assertions = True
-python_bindings = True
+python_bindings = False
 skip_all_tests = True
 
 llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi']

From 44d1800c0df6705d962b5abd8e1b2b4c7deff06d Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 24 Jan 2023 16:18:06 +0100
Subject: [PATCH 051/601] Python is still required as a build dep

...even when not using bindings
---
 easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
index 28274b11f14..dea2f244ad3 100644
--- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb
@@ -29,6 +29,8 @@ builddependencies = [
     ('CMake', '3.23.1'),
     ('Perl', '5.34.1'),
     ('elfutils', '0.187'),
+    # Including Python bindings would require this as a runtime dep
+    ('Python', '3.10.4'),
 ]
 dependencies = [
     # since Clang is a compiler, binutils is a runtime dependency too
@@ -38,8 +40,6 @@ dependencies = [
     ('ncurses', '6.3'),
     ('GMP', '6.2.1'),
     ('Z3', '4.10.2'),
-    # Including Python bindings would require this dep
-    # ('Python', '3.10.4'),
 ]
 
 # enabling RTTI makes the flang compiler need to link to libc++ so instead of

From 7678762f7fc6bd8904860a9371277e85bfe1efb5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 3 Feb 2023 17:17:41 +0000
Subject: [PATCH 052/601] adding easyconfigs:
 UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb and patches:
 UCC-CUDA-1.1.0_cuda_12_mem_ops.patch

---
 ...C-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb | 61 ++++++++++++
 .../UCC-CUDA-1.1.0_cuda_12_mem_ops.patch      | 99 +++++++++++++++++++
 2 files changed, 160 insertions(+)
 create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
 create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch

diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
new file mode 100644
index 00000000000..e607ff3eb14
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
@@ -0,0 +1,61 @@
+easyblock = 'ConfigureMake'
+
+name = 'UCC-CUDA'
+version = '1.1.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://www.openucx.org/'
+description = """UCC (Unified Collective Communication) is a collective
+communication operations API and library that is flexible, complete, and 
+feature-rich for current and emerging programming models and runtimes.
+
+This module adds the UCC CUDA support.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/openucx/ucc/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    '%(name)s-1.0.0_link_against_existing_UCC_libs.patch',
+    '%(name)s-%(version)s_cuda_12_mem_ops.patch',
+]
+checksums = [
+    {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'},
+    {'UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch':
+     '9fa11cf6779174f4e9048df5812096e4261e1769d465cc7f34a6354398876856'},
+    {'UCC-CUDA-1.1.0_cuda_12_mem_ops.patch': 'fc3ea1487d29dc626db2363ef5a79e7f0906f6a7507a363fa6167a812b143eb6'},
+]
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('Autotools', '20220317'),
+]
+
+dependencies = [
+    ('UCC', '1.1.0'),
+    ('CUDA',  '12.0.0', '', SYSTEM),
+    ('UCX-CUDA', '1.13.1', '-CUDA-%(cudaver)s'),
+    ('NCCL', '2.16.2', '-CUDA-%(cudaver)s'),
+]
+
+preconfigopts = "./autogen.sh && "
+
+buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1'
+installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install'
+
+# UCC_COMPONENT_PATH completely overrides $EBROOTUCC/lib/ucc so install symbolic links
+# to existing non CUDA related components
+postinstallcmds = ['for i in $EBROOTUCC/lib/ucc/*; do ln -s $i %(installdir)s/lib/ucc; done']
+
+sanity_check_paths = {
+    'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT],
+    'dirs': ['lib']
+}
+
+sanity_check_commands = ["ucc_info -c"]
+
+modextravars = {'UCC_COMPONENT_PATH': '%(installdir)s/lib/ucc'}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch
new file mode 100644
index 00000000000..36212b970db
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch
@@ -0,0 +1,99 @@
+Backported fix for CUDA 12 https://github.com/openucx/ucc/pull/700
+Essentially just removes the deprecated checks for CUDA MEM OPS as they are required in CUDA 12
+author: micketeer@gmail.com
+--- src/components/ec/cuda/ec_cuda.c.orig	2023-02-02 18:44:36.085221084 +0000
++++ src/components/ec/cuda/ec_cuda.c	2023-02-02 18:47:23.726819030 +0000
+@@ -205,11 +205,10 @@
+ {
+     ucc_ec_cuda_config_t *cfg = EC_CUDA_CONFIG;
+     ucc_status_t          status;
+-    int                   device, num_devices, attr;
++    int                   device, num_devices;
+     CUdevice              cu_dev;
+     CUresult              cu_st;
+     cudaError_t           cuda_st;
+-    const char           *cu_err_st_str;
+ 
+     ucc_ec_cuda.stream                   = NULL;
+     ucc_ec_cuda.stream_initialized       = 0;
+@@ -272,9 +271,14 @@
+     } else {
+         ucc_ec_cuda.strm_task_mode = UCC_EC_CUDA_TASK_MEM_OPS;
+         ucc_ec_cuda.post_strm_task = ucc_ec_cuda_post_driver_stream_task;
++#if CUDA_VERSION < 12000
++        CUresult cu_st;
++        CUdevice cu_dev;
++        int attr;
+ 
+         cu_st = cuCtxGetDevice(&cu_dev);
+         if (cu_st != CUDA_SUCCESS){
++            const char *cu_err_st_str;
+             cuGetErrorString(cu_st, &cu_err_st_str);
+             ec_debug(&ucc_ec_cuda.super, "cuCtxGetDevice() failed: %s",
+                      cu_err_st_str);
+@@ -297,6 +301,7 @@
+                      "CUDA MEM OPS are not supported or disabled");
+             return UCC_ERR_NOT_SUPPORTED;
+         }
++#endif
+     }
+     ucc_ec_cuda.task_strm_type = cfg->task_strm_type;
+     ucc_spinlock_init(&ucc_ec_cuda.init_spinlock, 0);
+--- src/components/tl/nccl/tl_nccl_context.c.orig	2023-02-03 15:17:09.358881676 +0000
++++ src/components/tl/nccl/tl_nccl_context.c	2023-02-03 17:04:31.680185749 +0000
+@@ -101,13 +101,14 @@
+         ucc_derived_of(config, ucc_tl_nccl_context_config_t);
+     int mem_ops_attr = 0;
+     ucc_status_t status;
+-    CUresult cu_st;
+-    CUdevice cu_dev;
+ 
+     UCC_CLASS_CALL_SUPER_INIT(ucc_tl_context_t, &tl_nccl_config->super,
+                               params->context);
+     memcpy(&self->cfg, tl_nccl_config, sizeof(*tl_nccl_config));
+     if (self->cfg.sync_type != UCC_TL_NCCL_COMPLETION_SYNC_TYPE_EVENT) {
++#if CUDA_VERSION < 12000
++        CUresult cu_st;
++        CUdevice cu_dev;
+         cu_st = cuCtxGetDevice(&cu_dev);
+         if (cu_st == CUDA_SUCCESS) {
+             cu_st = cuDeviceGetAttribute(&mem_ops_attr,
+@@ -116,6 +117,9 @@
+         } else {
+             tl_info(self->super.super.lib, "failed to get cuda device");
+         }
++#else
++        mem_ops_attr = 1;
++#endif
+         if (mem_ops_attr == 0) {
+             if (self->cfg.sync_type == UCC_TL_NCCL_COMPLETION_SYNC_TYPE_MEMOPS) {
+                 tl_error(self->super.super.lib, "memops not supported");
+--- config/m4/cuda.m4.orig	2023-02-03 17:04:44.367155175 +0000
++++ config/m4/cuda.m4	2023-02-03 17:06:26.110909987 +0000
+@@ -15,6 +15,11 @@
+ ARCH10="-gencode=arch=compute_75,code=sm_75"
+ ARCH11="-gencode=arch=compute_80,code=sm_80 \
+ -gencode=arch=compute_80,code=compute_80"
++ARCH111="-gencode=arch=compute_86,code=sm_86 \
++-gencode=arch=compute_86,code=compute_86"
++ARCH120="-gencode=arch=compute_90,code=sm_90 \
++-gencode=arch=compute_90,code=compute_90"
++
+ 
+ AC_DEFUN([CHECK_CUDA],[
+ AS_IF([test "x$cuda_checked" != "xyes"],
+@@ -104,8 +109,12 @@
+                [NVCC_CFLAGS="$NVCC_CFLAGS -O3 -g -DNDEBUG"])
+          AS_IF([test "x$cuda_happy" = "xyes"],
+                [AS_IF([test "x$with_nvcc_gencode" = "xdefault"],
+-                      [AS_IF([test $CUDA_MAJOR_VERSION -eq 11],
+-                             [NVCC_ARCH="${ARCH8} ${ARCH9} ${ARCH10} ${ARCH11}"])],
++                      [AS_IF([test $CUDA_MAJOR_VERSION -eq 12],
++                             [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110} ${ARCH111} ${ARCH120}"],
++                             [AS_IF([test $CUDA_MAJOR_VERSION -eq 11],
++                                   [AS_IF([test $CUDA_MINOR_VERSION -lt 1],
++                                           [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110}"],
++                                           [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110} ${ARCH111}"])])])],
+                       [NVCC_ARCH="$with_nvcc_gencode"])
+                 AC_SUBST([NVCC_ARCH], ["$NVCC_ARCH"])])
+          LDFLAGS="$save_LDFLAGS"

From 88129834ef3be48af724901e9e83e8f37e5fc31a Mon Sep 17 00:00:00 2001
From: Steven Vandenbrande <steven.vandenbrande@kuleuven.be>
Date: Thu, 9 Feb 2023 15:33:54 +0100
Subject: [PATCH 053/601] adding easyconfigs: Hypre-2.21.0-intel-2021a.eb,
 MUMPS-5.4.0-intel-2021a-metis.eb, PETSc-3.15.1-intel-2021a.eb,
 SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb and patches:
 PETSc_remove-mpiicc-show-quotes.patch

---
 .../h/Hypre/Hypre-2.21.0-intel-2021a.eb       | 21 ++++++++
 .../m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb  | 38 ++++++++++++++
 .../p/PETSc/PETSc-3.15.1-intel-2021a.eb       | 52 +++++++++++++++++++
 .../PETSc_remove-mpiicc-show-quotes.patch     | 12 +++++
 ...teSparse-5.10.1-intel-2021a-METIS-5.1.0.eb | 29 +++++++++++
 5 files changed, 152 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb
 create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb
 create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb
 create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch
 create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb

diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb
new file mode 100644
index 00000000000..900b8bfcad7
--- /dev/null
+++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb
@@ -0,0 +1,21 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'Hypre'
+version = '2.21.0'
+
+homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods'
+description = """Hypre is a library for solving large, sparse linear systems of equations on massively
+ parallel computers. The problems of interest arise in the simulation codes being developed at LLNL
+ and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences."""
+
+toolchain = {'name': 'intel', 'version': '2021a'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/hypre-space/hypre/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['e380f914fe7efe22afc44cdf553255410dc8a02a15b2e5ebd279ba88817feaf5']
+
+start_dir = 'src'
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb
new file mode 100644
index 00000000000..fa811d068f9
--- /dev/null
+++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb
@@ -0,0 +1,38 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'MUMPS'
+version = '5.4.0'
+versionsuffix = '-metis'
+
+homepage = 'https://graal.ens-lyon.fr/MUMPS/'
+description = "A parallel sparse direct solver"
+
+toolchain = {'name': 'intel', 'version': '2021a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://graal.ens-lyon.fr/MUMPS/']
+sources = ['%(name)s_%(version)s.tar.gz']
+patches = [
+    '%(name)s-%(version)s_shared-pord.patch',    # builds the shared libs of PORD
+    '%(name)s-%(version)s_shared-mumps.patch',   # builds shared libs of MUMPS
+]
+checksums = [
+    'c613414683e462da7c152c131cebf34f937e79b30571424060dd673368bbf627',  # MUMPS_5.4.0.tar.gz
+    '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170',  # MUMPS-5.4.0_shared-pord.patch
+    'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d',  # MUMPS-5.4.0_shared-mumps.patch
+]
+
+dependencies = [
+    ('SCOTCH', '6.1.0'),
+    ('METIS', '5.1.0'),
+]
+
+parallel = 1
+
+# fix 'Type mismatch between actual argument' errors with GCC 10.x
+prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && '
+
+buildopts = 'all SONAME_VERSION="%(version)s"'
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb
new file mode 100644
index 00000000000..e65a78b214e
--- /dev/null
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb
@@ -0,0 +1,52 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'PETSc'
+version = '3.15.1'
+
+homepage = 'https://www.mcs.anl.gov/petsc'
+description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
+ scalable (parallel) solution of scientific applications modeled by partial differential equations."""
+
+toolchain = {'name': 'intel', 'version': '2021a'}
+toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
+
+source_urls = [
+    'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+    'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'PETSc_ranlib-fix.patch',
+    'PETSc_remove-mpiicc-show-quotes.patch',
+]
+checksums = [
+    {'petsc-3.15.1.tar.gz': 'c0ac6566e69d1d70b431e07e7598e9de95e84891c2452db1367c846b75109deb'},
+    {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'},
+    {'PETSc_remove-mpiicc-show-quotes.patch': '917218e4244f579879cbea4a428d05a61b4266f65c23d9cdfb754d187066d62d'},
+]
+
+builddependencies = [('CMake', '3.20.1')]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('Boost', '1.76.0'),
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '6.1.0'),
+    ('MUMPS', '5.4.0', '-metis'),
+    ('SuiteSparse', '5.10.1', '-METIS-5.1.0'),
+    ('Hypre', '2.21.0'),
+]
+
+# enabling --with-mpi4py seems to be totally broken, leads to make errors like:
+# No rule to make target 'mpi4py-build'
+configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 '
+
+shared_libs = 1
+
+# only required when building PETSc in a SLURM job environment
+# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 '
+# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && "
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch
new file mode 100644
index 00000000000..07bb3ccc082
--- /dev/null
+++ b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch
@@ -0,0 +1,12 @@
+diff -Nru config/PETSc/Configure.py.back config/PETSc/Configure.py`
+--- config/PETSc/Configure.py.back	2023-02-09 14:59:14.086680000 +0100
++++ config/PETSc/Configure.py	2023-02-09 14:59:03.095892000 +0100
+@@ -251,7 +251,7 @@
+     compiler = self.setCompilers.getCompiler()
+     if [s for s in ['mpicc','mpiicc'] if os.path.basename(compiler).find(s)>=0]:
+       try:
+-        output   = self.executeShellCommand(compiler + ' -show', log = self.log)[0]
++        output   = self.executeShellCommand(compiler + ' -show', log = self.log)[0].replace('"', '')
+         compiler = output.split(' ')[0]
+         self.addDefine('MPICC_SHOW','"'+output.strip().replace('\n','\\\\n')+'"')
+       except:
diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
new file mode 100644
index 00000000000..d896b7962de
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
@@ -0,0 +1,29 @@
+name = 'SuiteSparse'
+version = '5.10.1'
+local_metis_ver = '5.1.0'
+versionsuffix = '-METIS-%s' % local_metis_ver
+
+homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries manipulate sparse matrices."""
+
+toolchain = {'name': 'intel', 'version': '2021a'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee']
+
+builddependencies = [
+    ('CMake', '3.20.1'),
+    ('M4', '1.4.18'),
+]
+
+dependencies = [
+    ('METIS', local_metis_ver),
+    ('MPFR', '4.1.0'),
+]
+
+# make sure that bin/demo can find libsuitesparseconfig.so.5 during build
+prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
+
+moduleclass = 'numlib'

From 3b65a6cb077dacb033df9346647d8184737b72a7 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 9 Feb 2023 16:48:31 +0100
Subject: [PATCH 054/601] Fix ELSI build and add missing foss versions

---
 .../e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb     | 39 ++++++++++++++++++
 .../e/ELSI/ELSI-2.5.0-foss-2019b.eb           | 38 ++++++++++++++++++
 .../e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb    |  6 ++-
 .../e/ELSI/ELSI-2.5.0-intel-2019b.eb          |  6 ++-
 .../ELSI-2.5.0_fix-compiler-detection.patch   | 40 +++++++++++++++++++
 .../e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb     |  2 +
 .../e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb    |  2 +
 .../ELSI-2.6.4_fix-compiler-detection.patch   | 36 +++++++++++++++++
 .../e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb     |  2 +
 .../e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb    |  2 +
 10 files changed, 171 insertions(+), 2 deletions(-)
 create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb
 create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb
 create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch
 create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch

diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb
new file mode 100644
index 00000000000..347ad480808
--- /dev/null
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb
@@ -0,0 +1,39 @@
+name = 'ELSI'
+version = '2.5.0'
+versionsuffix = '-PEXSI'
+
+homepage = 'https://wordpress.elsi-interchange.org/'
+description = """ELSI provides and enhances scalable, open-source software library solutions for
+ electronic structure calculations in  materials science, condensed matter physics, chemistry, and many other fields.
+ ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory.
+ The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
+"""
+
+toolchain = {'name': 'foss', 'version': '2019b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_fix-compiler-detection.patch']
+checksums = [
+    'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f',
+    '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5',
+]
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.3.2'),
+    ('CMake', '3.15.3'),
+]
+
+dependencies = [
+    ('ELPA', '2019.11.001'),
+    # SLEPc and internal PEXSI can't coexist due to conflicting dependencies
+    # ('SLEPc', '3.12.2', '-Python-3.7.4'),
+]
+
+build_internal_pexsi = True
+
+runtest = True
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb
new file mode 100644
index 00000000000..00a54e827fd
--- /dev/null
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb
@@ -0,0 +1,38 @@
+name = 'ELSI'
+version = '2.5.0'
+
+homepage = 'https://wordpress.elsi-interchange.org/'
+description = """ELSI provides and enhances scalable, open-source software library solutions for
+ electronic structure calculations in  materials science, condensed matter physics, chemistry, and many other fields.
+ ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory.
+ The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
+"""
+
+toolchain = {'name': 'foss', 'version': '2019b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_fix-compiler-detection.patch']
+checksums = [
+    'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f',
+    '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5',
+]
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.3.2'),
+    ('CMake', '3.15.3'),
+]
+
+dependencies = [
+    ('ELPA', '2019.11.001'),
+    ('SLEPc', '3.12.2', '-Python-3.7.4'),
+]
+
+# SLEPc and internal PEXSI can't coexist due to conflicting dependencies
+build_internal_pexsi = False
+
+runtest = True
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb
index 7a3d6a93e71..84704deb0c4 100644
--- a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb
@@ -14,7 +14,11 @@ toolchainopts = {'usempi': True, 'pic': True}
 
 source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f']
+patches = ['%(name)s-%(version)s_fix-compiler-detection.patch']
+checksums = [
+    'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f',
+    '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5',
+]
 
 builddependencies = [
     ('flex', '2.6.4'),
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb
index ca508d490f8..4ba1e4b7a8a 100644
--- a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb
@@ -13,7 +13,11 @@ toolchainopts = {'usempi': True, 'pic': True}
 
 source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f']
+patches = ['%(name)s-%(version)s_fix-compiler-detection.patch']
+checksums = [
+    'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f',
+    '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5',
+]
 
 builddependencies = [
     ('flex', '2.6.4'),
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch
new file mode 100644
index 00000000000..c61708a48f9
--- /dev/null
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch
@@ -0,0 +1,40 @@
+Let CMake search for the compilers and only fail if they are not found.
+See https://gitlab.com/elsi_project/elsi_interface/-/merge_requests/304
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index b8d22e53..f1570a8e 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -67,14 +67,18 @@ SET(INC_PATHS "" CACHE STRING "List of include directories")
+ SET(LIBS "" CACHE STRING "List of external libraries to be linked against")
+ 
+ ### Compilers ###
+-IF(NOT DEFINED CMAKE_Fortran_COMPILER)
++INCLUDE(CheckLanguage)
++
++CHECK_LANGUAGE(Fortran)
++IF(NOT CMAKE_Fortran_COMPILER)
+   MESSAGE(FATAL_ERROR "${MAGENTA}Fortran compiler must be set${COLORRESET}")
+ ELSE()
+   MESSAGE(STATUS "${GREEN}Fortran compiler${COLORRESET}: ${CMAKE_Fortran_COMPILER}")
+   ENABLE_LANGUAGE(Fortran)
+ ENDIF()
+ IF(ENABLE_PEXSI OR ENABLE_C_TESTS OR ELPA2_KERNEL STREQUAL "AVX512" OR ELPA2_KERNEL STREQUAL "AVX2" OR ELPA2_KERNEL STREQUAL "AVX")
+-  IF(NOT DEFINED CMAKE_C_COMPILER)
++  CHECK_LANGUAGE(C)
++  IF(NOT CMAKE_C_COMPILER)
+     MESSAGE(FATAL_ERROR "${MAGENTA}C compiler must be set${COLORRESET}")
+   ELSE()
+     MESSAGE(STATUS "${GREEN}C compiler${COLORRESET}: ${CMAKE_C_COMPILER}")
+@@ -82,7 +86,8 @@ IF(ENABLE_PEXSI OR ENABLE_C_TESTS OR ELPA2_KERNEL STREQUAL "AVX512" OR ELPA2_KER
+   ENDIF()
+ ENDIF()
+ IF(ENABLE_PEXSI)
+-  IF(NOT DEFINED CMAKE_CXX_COMPILER)
++  CHECK_LANGUAGE(CXX)
++  IF(NOT CMAKE_CXX_COMPILER)
+     MESSAGE(FATAL_ERROR "${MAGENTA}C++ compiler must be set${COLORRESET}")
+   ELSE()
+     MESSAGE(STATUS "${GREEN}C++ compiler${COLORRESET}: ${CMAKE_CXX_COMPILER}")
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb
index 332df2352b0..68020a6e291 100644
--- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb
@@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11
 sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'pexsi-1.2.0-mpi30.patch',
+    '%(name)s-%(version)s_fix-compiler-detection.patch',
     'ELSI-2.7.1_bison_3.7_compat.patch',
 ]
 checksums = [
     'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4',  # elsi-2.6.4.tar.gz
     'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb',  # pexsi-1.2.0-mpi30.patch
+    '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37',  # ELSI-2.6.4_fix-compiler-detection.patch
     '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb',  # ELSI-2.7.1_bison_3.7_compat.patch
 ]
 
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb
index 800d33b16dc..ff84be63e3a 100644
--- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb
@@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11
 sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'pexsi-1.2.0-mpi30.patch',
+    '%(name)s-%(version)s_fix-compiler-detection.patch',
     'ELSI-2.7.1_bison_3.7_compat.patch',
 ]
 checksums = [
     'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4',  # elsi-2.6.4.tar.gz
     'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb',  # pexsi-1.2.0-mpi30.patch
+    '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37',  # ELSI-2.6.4_fix-compiler-detection.patch
     '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb',  # ELSI-2.7.1_bison_3.7_compat.patch
 ]
 
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch
new file mode 100644
index 00000000000..5e931749a78
--- /dev/null
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch
@@ -0,0 +1,36 @@
+Let CMake search for the compilers and only fail if they are not found.
+See https://gitlab.com/elsi_project/elsi_interface/-/merge_requests/304
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3f016ec7..9aaf8395 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -55,18 +55,23 @@ SET(INC_PATHS "" CACHE STRING "List of include directories")
+ SET(LIBS "" CACHE STRING "List of external libraries to be linked against")
+ 
+ ### Compilers ###
+-IF(NOT DEFINED CMAKE_Fortran_COMPILER)
++INCLUDE(CheckLanguage)
++
++CHECK_LANGUAGE(Fortran)
++IF(NOT CMAKE_Fortran_COMPILER)
+   MESSAGE(FATAL_ERROR "${MAGENTA}Fortran compiler must be set${COLORRESET}")
+ ENDIF()
+ ENABLE_LANGUAGE(Fortran)
+ 
+-IF(NOT DEFINED CMAKE_C_COMPILER)
++CHECK_LANGUAGE(C)
++IF(NOT CMAKE_C_COMPILER)
+   MESSAGE(FATAL_ERROR "${MAGENTA}C compiler must be set${COLORRESET}")
+ ENDIF()
+ ENABLE_LANGUAGE(C)
+ 
+ IF(ENABLE_PEXSI)
+-  IF(NOT DEFINED CMAKE_CXX_COMPILER)
++  CHECK_LANGUAGE(CXX)
++  IF(NOT CMAKE_CXX_COMPILER)
+     MESSAGE(FATAL_ERROR "${MAGENTA}C++ compiler must be set${COLORRESET}")
+   ENDIF()
+   ENABLE_LANGUAGE(CXX)
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb
index 97218cbf6a8..1995ff511e0 100644
--- a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb
@@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03
 sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'pexsi-1.2.0-mpi30.patch',
+    '%(name)s-2.6.4_fix-compiler-detection.patch',
     'ELSI-2.7.1_bison_3.7_compat.patch',
 ]
 checksums = [
     '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d',  # elsi-2.7.1.tar.gz
     'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb',  # pexsi-1.2.0-mpi30.patch
+    '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37',  # ELSI-2.6.4_fix-compiler-detection.patch
     '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb',  # ELSI-2.7.1_bison_3.7_compat.patch
 ]
 
diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb
index 94759abacfc..6e3baf0eb4c 100644
--- a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb
+++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb
@@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03
 sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'pexsi-1.2.0-mpi30.patch',
+    '%(name)s-2.6.4_fix-compiler-detection.patch',
     'ELSI-2.7.1_bison_3.7_compat.patch',
 ]
 checksums = [
     '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d',  # elsi-2.7.1.tar.gz
     'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb',  # pexsi-1.2.0-mpi30.patch
+    '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37',  # ELSI-2.6.4_fix-compiler-detection.patch
     '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb',  # ELSI-2.7.1_bison_3.7_compat.patch
 ]
 

From 5cbe0e9c455ee41619cf4bc953320c32a7517156 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Tue, 7 Feb 2023 15:00:43 +0100
Subject: [PATCH 055/601] adding easyconfigs:
 PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb,
 NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb,
 UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb,
 magma-2.6.2-foss-2021b-CUDA-11.5.2.eb, cuDNN-8.4.1.50-CUDA-11.5.2.eb,
 CUDA-11.5.2.eb

---
 easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb   |  26 +++
 .../c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb     |  41 +++++
 .../magma-2.6.2-foss-2021b-CUDA-11.5.2.eb     |  42 +++++
 .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb |  23 +++
 .../PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb  | 156 ++++++++++++++++++
 ...-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb |  42 +++++
 6 files changed, 330 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb
 create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb
 create mode 100644 easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb
 create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb
 create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
 create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb

diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb
new file mode 100644
index 00000000000..bc5895712e0
--- /dev/null
+++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb
@@ -0,0 +1,26 @@
+name = 'CUDA'
+version = '11.5.2'
+local_nv_version = '495.29.05'
+
+homepage = 'https://developer.nvidia.com/cuda-toolkit'
+description = """CUDA (formerly Compute Unified Device Architecture) is a parallel
+ computing platform and programming model created by NVIDIA and implemented by the
+ graphics processing units (GPUs) that they produce. CUDA gives developers access
+ to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/']
+sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version]
+checksums = [
+    {
+        'cuda_%%(version)s_%s_linux.run' % local_nv_version:
+            '74959abf02bcba526f0a3aae322c7641b25da040ccd6236d07038f81997b73a6',
+        'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version:
+            '45c468f430436b3e95d5e485a6ba0ec1fa2b23dc6c551c1307b79996ecf0a7ed',
+        'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version:
+            '31337c8bdc224fa1bd07bc4b6a745798392428118cc8ea0fa4446ee4ad47dd30',
+    }
+]
+
+moduleclass = 'system'
diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb
new file mode 100644
index 00000000000..2a974448907
--- /dev/null
+++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb
@@ -0,0 +1,41 @@
+name = 'cuDNN'
+version = '8.4.1.50'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://developer.nvidia.com/cudnn'
+description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is
+a GPU-accelerated library of primitives for deep neural networks."""
+
+toolchain = SYSTEM
+
+# note: cuDNN 8.4.1 is not specific to CUDA 11.6,
+# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions
+local_short_ver = '.'.join(version.split('.')[:3])
+source_urls = [
+    'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/11.6/' % local_short_ver,
+]
+sources = ['%(namelower)s-linux-%(cudnnarch)s-%(version)s_cuda11.6-archive.tar.xz']
+checksums = [
+    {
+        '%(namelower)s-linux-x86_64-%(version)s_cuda11.6-archive.tar.xz':
+            'ec96d2376d81fca42bdd3d4c3d705a99b29a065bab57f920561c763e29c67d01',
+        '%(namelower)s-linux-ppc64le-%(version)s_cuda11.6-archive.tar.xz':
+            '8b806cbfdc81352bf76716d1e53b42537665d110c6ffc068be910505c10e1b98',
+        '%(namelower)s-linux-sbsa-%(version)s_cuda11.6-archive.tar.xz':
+            '0b1b9fac5b78974e2fdaaa74843db18f636ce8f3d999d62ff2a615b9978fc360',
+    }
+]
+
+dependencies = [('CUDA', '11.5.2')]
+
+sanity_check_paths = {
+    'files': [
+        'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a',
+        'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a',
+        'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a',
+        'lib64/libcudnn.%s' % SHLIB_EXT
+    ],
+    'dirs': ['include', 'lib64'],
+}
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb
new file mode 100644
index 00000000000..3f167192cb4
--- /dev/null
+++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb
@@ -0,0 +1,42 @@
+easyblock = "CMakeMake"
+
+name = 'magma'
+version = '2.6.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://icl.cs.utk.edu/magma/'
+description = """The MAGMA project aims to develop a dense linear algebra library similar to
+ LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/']
+sources = [SOURCE_TAR_GZ]
+patches = ['magma-2.6.1_allow-all-sms.patch']
+checksums = [
+    '75b554dab00903e2d10b972c913e50e7f88cbc62f3ae432b5a086c7e4eda0a71',  # magma-2.6.2.tar.gz
+    'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738',  # magma-2.6.1_allow-all-sms.patch
+]
+
+builddependencies = [
+    ('CMake', '3.21.1'),
+]
+
+dependencies = [
+    ('CUDA', '11.5.2', '', SYSTEM),
+]
+
+# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
+cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6']
+# make sure both static and shared libs are built
+configopts = [
+    '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF')
+]
+
+sanity_check_paths = {
+    'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb
new file mode 100644
index 00000000000..e3a29b13334
--- /dev/null
+++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb
@@ -0,0 +1,23 @@
+name = 'NCCL'
+version = '2.10.3'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://developer.nvidia.com/nccl'
+description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective
+communication primitives that are performance optimized for NVIDIA GPUs."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+github_account = 'NVIDIA'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s-1.tar.gz']
+checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5']
+
+builddependencies = [('binutils', '2.37')]
+
+dependencies = [
+    ('CUDA', '11.5.2', '', SYSTEM),
+    ('UCX-CUDA', '1.11.2', versionsuffix),
+]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
new file mode 100644
index 00000000000..888bdda4b4f
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -0,0 +1,156 @@
+name = 'PyTorch'
+version = '1.12.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://pytorch.org/'
+description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration.
+PyTorch is a deep learning framework that puts Python first."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = [GITHUB_RELEASE]
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+
+patches = [
+    'PyTorch-1.7.0_avoid-nan-in-test-torch.patch',
+    'PyTorch-1.7.0_disable-dev-shm-test.patch',
+    'PyTorch-1.10.0_fix-kineto-crash.patch',
+    'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch',
+    'PyTorch-1.10.0_fix-test-model_dump.patch',
+    'PyTorch-1.10.0_fix-vsx-vector-functions.patch',
+    'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch',
+    'PyTorch-1.11.0_fix-fsdp-fp16-test.patch',
+    'PyTorch-1.11.0_fix-test_utils.patch',
+    'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch',
+    'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
+    'PyTorch-1.11.0_install-vsx-vec-headers.patch',
+    'PyTorch-1.11.1_skip-test_init_from_local_shards.patch',
+    'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch',
+    'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
+    'PyTorch-1.12.1_fix-skip-decorators.patch',
+    'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
+    'PyTorch-1.12.1_fix-test_wishart_log_prob.patch',
+    'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch',
+    'PyTorch-1.12.1_fix-TestTorch.test_to.patch',
+    'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch',
+    'PyTorch-1.12.1_fix-vsx-vector-funcs.patch',
+    'PyTorch-1.12.1_fix-vsx-loadu.patch',
+    'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch',
+    'PyTorch-1.12.1_increase-tolerance-test_ops.patch',
+    'PyTorch-1.12.1_no-cuda-stubs-rpath.patch',
+    'PyTorch-1.12.1_python-3.10-annotation-fix.patch',
+    'PyTorch-1.12.1_python-3.10-compat.patch',
+    'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch',
+    'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
+    'PyTorch-1.12.1_skip-failing-grad-test.patch',
+    'PyTorch-1.12.1_skip-test_round_robin.patch',
+]
+checksums = [
+    '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
+    'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18',  # PyTorch-1.7.0_avoid-nan-in-test-torch.patch
+    '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a',  # PyTorch-1.7.0_disable-dev-shm-test.patch
+    # PyTorch-1.10.0_fix-kineto-crash.patch
+    'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb',
+    # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch
+    '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707',
+    # PyTorch-1.10.0_fix-test-model_dump.patch
+    '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557',
+    # PyTorch-1.10.0_fix-vsx-vector-functions.patch
+    '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312',
+    # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch
+    '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2',
+    'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13',  # PyTorch-1.11.0_fix-fsdp-fp16-test.patch
+    '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861',  # PyTorch-1.11.0_fix-test_utils.patch
+    # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch
+    '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953',
+    # PyTorch-1.11.0_increase-distributed-test-timeout.patch
+    '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f',
+    'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
+    # PyTorch-1.11.1_skip-test_init_from_local_shards.patch
+    '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7',
+    # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch
+    'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089',
+    # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
+    'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab',
+    'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c',  # PyTorch-1.12.1_fix-skip-decorators.patch
+    # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch
+    '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83',
+    # PyTorch-1.12.1_fix-test_wishart_log_prob.patch
+    'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45',
+    # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch
+    '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2',
+    '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535',  # PyTorch-1.12.1_fix-TestTorch.test_to.patch
+    # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch
+    '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d',
+    'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2',  # PyTorch-1.12.1_fix-vsx-vector-funcs.patch
+    '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2',  # PyTorch-1.12.1_fix-vsx-loadu.patch
+    # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch
+    '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695',
+    # PyTorch-1.12.1_increase-tolerance-test_ops.patch
+    '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb',
+    '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6',  # PyTorch-1.12.1_no-cuda-stubs-rpath.patch
+    # PyTorch-1.12.1_python-3.10-annotation-fix.patch
+    '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7',
+    '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67',  # PyTorch-1.12.1_python-3.10-compat.patch
+    # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch
+    'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d',
+    # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch
+    'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39',
+    '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
+    # PyTorch-1.12.1_skip-test_round_robin.patch
+    '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349',
+]
+
+osdependencies = [OS_PKG_IBVERBS_DEV]
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+    ('hypothesis', '6.14.6'),
+]
+
+dependencies = [
+    ('CUDA', '11.5.2', '', SYSTEM),
+    ('Ninja', '1.10.2'),  # Required for JIT compilation of C++ extensions
+    ('Python', '3.9.6'),
+    ('protobuf', '3.17.3'),
+    ('protobuf-python', '3.17.3'),
+    ('pybind11', '2.7.1'),
+    ('SciPy-bundle', '2021.10'),
+    ('typing-extensions', '3.10.0.2'),
+    ('PyYAML', '5.4.1'),
+    ('MPFR', '4.1.0'),
+    ('GMP', '6.2.1'),
+    ('numactl', '2.0.14'),
+    ('FFmpeg', '4.3.2'),
+    ('Pillow', '8.3.2'),
+    ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM),
+    ('magma', '2.6.2', '-CUDA-%(cudaver)s'),
+    ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'),
+    ('expecttest', '0.1.3'),
+]
+
+# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
+cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6']
+
+excluded_tests = {
+    '': [
+        # This test seems to take too long on NVIDIA Ampere at least.
+        'distributed/test_distributed_spawn',
+        # Those 2 abort on some machines. Skip for now
+        'distributed/fsdp/test_fsdp_input',
+        'distributed/fsdp/test_fsdp_mixed_precision',
+    ]
+}
+
+runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error  --verbose %(excluded_tests)s'
+
+# The readelf sanity check command can be taken out once the TestRPATH test from
+# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite
+local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT
+sanity_check_commands = [
+    "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2,
+]
+
+tests = ['PyTorch-check-cpp-extension.py']
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb
new file mode 100644
index 00000000000..3748b1ba66a
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb
@@ -0,0 +1,42 @@
+easyblock = 'EB_UCX_Plugins'
+
+name = 'UCX-CUDA'
+version = '1.11.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'http://www.openucx.org/'
+description = """Unified Communication X
+An open-source production grade communication framework for data centric
+and high-performance applications
+
+This module adds the UCX CUDA support.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s']
+sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}]
+patches = [
+    '%(name)s-1.11.0_link_against_existing_UCX_libs.patch',
+]
+checksums = [
+    {'ucx-1.11.2.tar.gz': 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df'},
+    {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch':
+     '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'},
+]
+
+builddependencies = [
+    ('binutils', '2.37'),
+    ('Autotools', '20210726'),
+    ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('UCX', version),
+    ('CUDA',  '11.5.2', '', SYSTEM),
+    ('GDRCopy', '2.3'),
+]
+
+moduleclass = 'lib'

From 0edb086839e31e3205e2c0f8699bac4121ac3df4 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Fri, 10 Feb 2023 17:29:01 +0100
Subject: [PATCH 056/601] Skip distributions/test_constraints

---
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb          | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
index 888bdda4b4f..c77bc6a7b31 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -136,6 +136,8 @@ excluded_tests = {
     '': [
         # This test seems to take too long on NVIDIA Ampere at least.
         'distributed/test_distributed_spawn',
+        # Broken on CUDA 11.5+(?): https://github.com/pytorch/pytorch/issues/75375
+        'distributions/test_constraints',
         # Those 2 abort on some machines. Skip for now
         'distributed/fsdp/test_fsdp_input',
         'distributed/fsdp/test_fsdp_mixed_precision',

From 5f7ba1239d3fbafa5eada049296946165e986fc9 Mon Sep 17 00:00:00 2001
From: Steven Vandenbrande <steven.vandenbrande@kuleuven.be>
Date: Tue, 14 Feb 2023 17:13:20 +0100
Subject: [PATCH 057/601] Add header to PETSc patch for mpiicc

---
 .../p/PETSc/PETSc_remove-mpiicc-show-quotes.patch           | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch
index 07bb3ccc082..0286368966e 100644
--- a/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch
+++ b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch
@@ -1,3 +1,9 @@
+The PETSc configuration script relies on the output of the command
+"mpicc/mpiicc -show". For some versions of mpiicc, that command prints
+include and link paths between double quotes, which confuses the PETSc
+configuration script. This patch removes the double quotes again and should
+only be necessary when using mpiicc newer than 2021a.
+Author: Steven Vandenbrande
 diff -Nru config/PETSc/Configure.py.back config/PETSc/Configure.py`
 --- config/PETSc/Configure.py.back	2023-02-09 14:59:14.086680000 +0100
 +++ config/PETSc/Configure.py	2023-02-09 14:59:03.095892000 +0100

From bb161d3a1274e5d3a2f6ef3962e7a5fb2a7b1e7f Mon Sep 17 00:00:00 2001
From: Steven Vandenbrande <steven.vandenbrande@kuleuven.be>
Date: Tue, 14 Feb 2023 17:59:52 +0100
Subject: [PATCH 058/601] Update checksum after adding comment to patch file

---
 easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb
index e65a78b214e..75d34f53c6c 100644
--- a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb
@@ -23,7 +23,7 @@ patches = [
 checksums = [
     {'petsc-3.15.1.tar.gz': 'c0ac6566e69d1d70b431e07e7598e9de95e84891c2452db1367c846b75109deb'},
     {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'},
-    {'PETSc_remove-mpiicc-show-quotes.patch': '917218e4244f579879cbea4a428d05a61b4266f65c23d9cdfb754d187066d62d'},
+    {'PETSc_remove-mpiicc-show-quotes.patch': 'e6ccd7ab33d806f1e635f536d94c98b7aa36f6462d6a0f9f71b177f6ed23f09e'},
 ]
 
 builddependencies = [('CMake', '3.20.1')]

From b1954252cede0da74d9a9e5656b7e93f13172d0c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 20 Feb 2023 17:36:41 +0100
Subject: [PATCH 059/601] adding easyconfigs: HTSplotter-0.15-foss-2022a.eb

---
 .../HTSplotter/HTSplotter-0.15-foss-2022a.eb  | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb

diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb
new file mode 100644
index 00000000000..98f87e55a48
--- /dev/null
+++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb
@@ -0,0 +1,51 @@
+easyblock = 'PythonBundle'
+
+name = 'HTSplotter'
+version = '0.15'
+
+homepage = 'https://github.com/CBIGR/HTSplotter'
+description = """HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro
+perturbation screens."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+    ('h5py', '3.7.0'),
+    ('Seaborn', '0.12.1'),
+    ('tqdm', '4.64.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('minio', '7.1.13', {
+        'checksums': ['8828615a20cde82df79c5a52005252ad29bb022cde25177a4a43952a04c3222c'],
+    }),
+    ('pypdf', '3.4.1', {
+        'checksums': ['8b0badc787062e8fb0d8393eb2a76903717fb24e5cc84e2b03cde5ac3881700f'],
+        # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x
+        'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' pypdf/_encryption.py && ",
+    }),
+    ('PyPDF2', '3.0.1', {
+        'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'],
+        # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x
+        'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' PyPDF2/_encryption.py && ",
+        'modulename': 'PyPDF2',
+    }),
+    ('PyPDF3', '1.0.6', {
+        'checksums': ['c946f3273419e37258e35e72273f49904ab15723d87a761c1115ef99799f8c5f'],
+        'modulename': 'PyPDF3',
+    }),
+    (name, version, {
+        'checksums': ['9504709ac2d04dbcd0694ca0370a44b7e302b667771fb492b596d9662a2a85a9'],
+        'modulename': 'HTSplotter',
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 23dfac778ecae7cc6f7859a2c20fc8da2d9d585a Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 22 Feb 2023 12:14:19 +0000
Subject: [PATCH 060/601] adding easyconfigs:
 libsigc++-2.12.0-GCCcore-11.3.0.eb

---
 .../libsigc++-2.12.0-GCCcore-11.3.0.eb        | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..d4470b7f612
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'libsigc++'
+version = '2.12.0'
+
+homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
+description = """The libsigc++ package implements a typesafe callback system for standard C++."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('Autotools', '20220317'),
+    ('Doxygen', '1.9.4'),
+    ('Graphviz', '5.0.0'),
+    ('libxslt', '1.1.34'),
+    ('mm-common', '1.0.5'),
+]
+
+preconfigopts = "./autogen.sh && "
+configopts = '--disable-documentation '
+
+sanity_check_paths = {
+    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From 9fd00d18883b891308555aa41de6da0f5f85f9ea Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 22 Feb 2023 12:22:11 +0000
Subject: [PATCH 061/601] version 3.4.0 added

---
 .../libsigc++-3.4.0-GCCcore-11.3.0.eb         | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..be3a0fa23e2
--- /dev/null
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'libsigc++'
+version = '3.4.0'
+
+homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
+description = """The libsigc++ package implements a typesafe callback system 
+for standard C++."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['02e2630ffb5ce93cd52c38423521dfe7063328863a6e96d41d765a6116b8707e']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('Graphviz', '5.0.0'),
+    ('libxslt', '1.1.34'),
+    ('mm-common', '1.0.5'),
+    ('CMake', '3.24.3'),
+]
+
+preconfigopts = "./autogen.sh && "
+configopts = '--disable-documentation '
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From caa7e1d4c1731737831688558b6221fb21ea5c51 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 22 Feb 2023 12:24:44 +0000
Subject: [PATCH 062/601] adding easyconfigs: mandrake-1.2.2-foss-2022a.eb

---
 .../m/mandrake/mandrake-1.2.2-foss-2022a.eb   | 53 +++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
new file mode 100644
index 00000000000..6b72810418d
--- /dev/null
+++ b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
@@ -0,0 +1,53 @@
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'PythonBundle'
+
+name = 'mandrake'
+version = '1.2.2'
+
+homepage = ' https://mandrake.readthedocs.io'
+description = """Fast visualisation of the population structure of pathogens 
+using Stochastic Cluster Embedding."""
+
+citing = """Lees JA, Tonkin-Hill G, Yang Z, Corander J. Mandrake: visualizing
+microbial population structure by embedding millions of genomes into a
+low-dimensional representation.
+Philosophical Transactions of The Royal Society B. 2022;377: 20210237.
+https://doi.org/10.1098/rstb.2021.0237"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('scikit-learn', '1.1.2'),
+    ('plotly.py', '5.12.0'),
+    ('pandas', '1.5.3'),
+    ('matplotlib', '3.5.2'),
+    ('HDBSCAN', '0.8.29'),
+    ('h5py', '3.7.0'),
+    ('pp-sketchlib', '2.1.1'),
+    ('pybind11', '2.9.2'),
+    ('Eigen', '3.4.0'),
+    ('Boost', '1.79.0'),
+    ('tqdm', '4.64.0'),
+    ('FFmpeg', '4.4.2'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/bacpop/mandrake/archive'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['5bbdde903252e2812d4ba484ae474ccc75efbaaf0ace7fe6f37a90e44fe3f0e5'],
+    }),
+]
+
+moduleclass = 'bio'

From b1ce0458cbeb7b92d9afa81c59f1d13e22d855a5 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 22 Feb 2023 12:32:45 +0000
Subject: [PATCH 063/601] adding easyconfigs: pp-sketchlib-2.1.1-foss-2022a.eb

---
 .../pp-sketchlib-2.1.1-foss-2022a.eb          | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb
new file mode 100644
index 00000000000..00174adc9d0
--- /dev/null
+++ b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb
@@ -0,0 +1,44 @@
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'PythonBundle'
+
+name = 'pp-sketchlib'
+version = '2.1.1'
+
+homepage = ' https://mandrake.readthedocs.io'
+description = """Library of sketching functions used by PopPUNK"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('h5py', '3.7.0'),
+    ('HDF5', '1.12.2'),
+    ('pybind11', '2.9.2'),
+    ('Eigen', '3.4.0'),
+    ('Boost', '1.79.0'),
+    ('nlohmann_json', '3.10.5'),
+    ('HighFive', '2.6.2'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('docopt', '0.6.2', {
+        'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/bacpop/pp-sketchlib/archive'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['b42acf0a58ea3225e3fe95adc8fc165578832c58e6f5b6fb3f7817655e0a9f30'],
+    }),
+]
+
+moduleclass = 'vis'

From 438320f86c0ee8ed85d3e7142c920b7d339067e4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Feb 2023 16:38:37 +0100
Subject: [PATCH 064/601] use better way to run 'pip check' in Raven easyconfig

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index ecf094af5d5..6694394fef7 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -54,7 +54,7 @@ sanity_check_paths = {
 }
 
 sanity_check_commands = [
-    "pip check",
+    "export PYTHONNOUSERSITE=1 && python%(pyshortver)s -m pip check",
     "raven --help"
 ]
 

From 0678a004ba36b1c0f8b295aba8c618e38bc772f8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 24 Feb 2023 16:50:18 +0100
Subject: [PATCH 065/601] use raw string in Raven easyconfig

---
 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index 6694394fef7..82f6b075da7 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -40,7 +40,7 @@ exts_list = [
         'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'],
         'sources': ['%(version)s.tar.gz'],
         'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'],
-        'preinstallopts': 'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \
+        'preinstallopts': r'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \
             "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",\
             "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|\' setup.py && '
     }),

From d788813283ee101259b414275e51cb90168e3bb6 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 28 Feb 2023 11:28:18 +0000
Subject: [PATCH 066/601] CMake used for 3.4.0, version 2.10.8 removed

---
 .../libsigc++-2.12.0-GCCcore-11.3.0.eb        | 32 -------------------
 .../libsigc++-3.4.0-GCCcore-11.3.0.eb         | 11 ++++---
 2 files changed, 6 insertions(+), 37 deletions(-)
 delete mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb
deleted file mode 100644
index d4470b7f612..00000000000
--- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb
+++ /dev/null
@@ -1,32 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'libsigc++'
-version = '2.12.0'
-
-homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/'
-description = """The libsigc++ package implements a typesafe callback system for standard C++."""
-
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
-toolchainopts = {'pic': True}
-
-source_urls = [FTPGNOME_SOURCE]
-sources = [SOURCELOWER_TAR_XZ]
-
-builddependencies = [
-    ('binutils', '2.38'),
-    ('Autotools', '20220317'),
-    ('Doxygen', '1.9.4'),
-    ('Graphviz', '5.0.0'),
-    ('libxslt', '1.1.34'),
-    ('mm-common', '1.0.5'),
-]
-
-preconfigopts = "./autogen.sh && "
-configopts = '--disable-documentation '
-
-sanity_check_paths = {
-    'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],
-    'dirs': [],
-}
-
-moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb
index be3a0fa23e2..2547b201764 100644
--- a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb
@@ -1,4 +1,7 @@
-easyblock = 'ConfigureMake'
+# Updated to CMakeMake
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'CMakeMake'
 
 name = 'libsigc++'
 version = '3.4.0'
@@ -22,10 +25,8 @@ builddependencies = [
     ('CMake', '3.24.3'),
 ]
 
-preconfigopts = "./autogen.sh && "
-configopts = '--disable-documentation '
-
-runtest = 'check'
+test_cmd = 'ctest'
+runtest = '-j'
 
 sanity_check_paths = {
     'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT],

From 99ea1c389b3532c9045243ade09eccf5f1f1e4cd Mon Sep 17 00:00:00 2001
From: Jiri Furst <Jiri.Furst@fs.cvut.cz>
Date: Wed, 1 Mar 2023 15:55:54 +0100
Subject: [PATCH 067/601] adding easyconfigs: ParaView-5.11.0-foss-2022b-mpi.eb

---
 .../ParaView-5.11.0-foss-2022b-mpi.eb         | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb

diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb
new file mode 100644
index 00000000000..8eed5565c1b
--- /dev/null
+++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb
@@ -0,0 +1,58 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+easyblock = 'CMakeMake'
+
+name = 'ParaView'
+version = '5.11.0'
+versionsuffix = '-mpi'
+
+homepage = 'https://www.paraview.org'
+description = "ParaView is a scientific parallel visualizer."
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile='
+source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix]
+sources = ["%(name)s-v%(version)s.tar.gz"]
+checksums = ['68b1c6d15dd67ec442f964460c56212417e8af2a96763001f8548eb3cbc5ce87']
+
+builddependencies = [('CMake', '3.24.3')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('XZ', '5.2.7'),
+    ('HDF5', '1.14.0'),
+    ('netCDF', '4.9.0'),
+    ('libGLU', '9.0.2'),
+    ('X11', '20221110'),
+    ('Mesa', '22.2.4'),
+    ('Qt5', '5.15.7'),
+    ('zlib', '1.2.12'),
+    ('FFmpeg', '5.1.2'),
+    ('Szip', '2.1.1'),
+]
+
+# Paraview
+configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON '
+configopts += '-DPARAVIEW_USE_MPI=ON '
+configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON '
+configopts += '-DPARAVIEW_USE_PYTHON=ON '
+configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON '
+
+# OpenGL & Mesa
+configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT
+configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include '
+
+sanity_check_paths = {
+    'files': ['bin/paraview', 'bin/pvpython'],
+    'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['python -c "import paraview"']
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'vis'

From c6cafb07b7b3002d09c585de3b6bd24899887933 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 6 Mar 2023 17:42:52 +0000
Subject: [PATCH 068/601] URL of homepage corrected

---
 .../easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb
index 00174adc9d0..ee3db5ffcf2 100644
--- a/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb
@@ -5,7 +5,7 @@ easyblock = 'PythonBundle'
 name = 'pp-sketchlib'
 version = '2.1.1'
 
-homepage = ' https://mandrake.readthedocs.io'
+homepage = 'https://github.com/bacpop/pp-sketchlib'
 description = """Library of sketching functions used by PopPUNK"""
 
 toolchain = {'name': 'foss', 'version': '2022a'}

From 46a69d54aa9332b0b681f56fc37365fce615dedc Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 6 Mar 2023 17:50:18 +0000
Subject: [PATCH 069/601] Blank in URL removed

---
 easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
index 6b72810418d..686bc673215 100644
--- a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
@@ -5,7 +5,7 @@ easyblock = 'PythonBundle'
 name = 'mandrake'
 version = '1.2.2'
 
-homepage = ' https://mandrake.readthedocs.io'
+homepage = 'https://mandrake.readthedocs.io'
 description = """Fast visualisation of the population structure of pathogens 
 using Stochastic Cluster Embedding."""
 

From d93b69305cffb2eb515d2bfc76153769e3d40fa8 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Tue, 7 Mar 2023 16:08:52 +0000
Subject: [PATCH 070/601] adding easyconfigs: ont-guppy-6.4.6-CUDA-11.7.0.eb,
 ont-guppy-6.4.6.eb

---
 .../ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb  | 38 +++++++++++++++++++
 .../o/ont-guppy/ont-guppy-6.4.6.eb            | 32 ++++++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb

diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..bc2f11eb6df
--- /dev/null
+++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb
@@ -0,0 +1,38 @@
+# Author: Jasper Grimm (UoY)
+easyblock = 'Tarball'
+
+name = 'ont-guppy'
+version = '6.4.6'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol'
+description = """
+Guppy is a bioinformatics toolkit that enables real-time basecalling and several
+ post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms.
+
+ For Research Use Only
+"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis']
+sources = ['%(name)s_%(version)s_linux64.tar.gz']
+checksums = ['a633b2f0712781ff303a4c8fecb08d5e5603c755d6c445a6181ab11930f5bd63']
+
+dependencies = [
+    ('CUDA', '11.7.0'),
+]
+
+_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex',
+                                  'basecaller_supervisor', 'basecall_server']]
+_libs = ['lib/libvbz_hdf_plugin.a']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _bins] + _libs,
+    'dirs': ['data'],
+}
+
+# requires libcuda.so to be present, else it exits with code 127
+# sanity_check_commands = ['%s --help' % x for x in _bins]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb
new file mode 100644
index 00000000000..be022994765
--- /dev/null
+++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb
@@ -0,0 +1,32 @@
+# Author: Jasper Grimm (UoY)
+easyblock = 'Tarball'
+
+name = 'ont-guppy'
+version = '6.4.6'
+
+homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol'
+description = """
+Guppy is a bioinformatics toolkit that enables real-time basecalling and several
+ post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms.
+
+ For Research Use Only
+"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis']
+sources = ['%(name)s-cpu_%(version)s_linux64.tar.gz']
+checksums = ['5c454a1d91124ff6da1618d08cae999b0091897e7f20e3dba09038303a259bef']
+
+_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex',
+                                  'basecaller_supervisor', 'basecall_server']]
+_libs = ['lib/libvbz_hdf_plugin.a']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _bins] + _libs,
+    'dirs': ['data'],
+}
+
+sanity_check_commands = ['%s --help' % x for x in _bins]
+
+moduleclass = 'bio'

From 0da2dc49cda15a033403c5f511185b4a8ef02bfb Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Wed, 8 Mar 2023 11:43:02 +0100
Subject: [PATCH 071/601] adding easyconfigs:
 libWallModelledLES-0.6.1-foss-2021b.eb

---
 .../libWallModelledLES-0.6.1-foss-2021b.eb    | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb

diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
new file mode 100644
index 00000000000..cf48519506d
--- /dev/null
+++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
@@ -0,0 +1,45 @@
+name = "libWallModelledLES"
+version = "0.6.1"
+easyblock = "Binary"
+
+homepage = "https://bitbucket.org/lesituu/libwallmodelledles/"
+description = """libWallModelledLES is a library based on OpenFOAM® technology,
+extending the capabilities of OpenFOAM in the area of wall-modelled LES (WMLES).
+This is a turbulence modelling methodology, which allows to make LES cheaper
+by not resolving the inner region of turbulent boundary layers."""
+
+toolchain = {"name": "foss", "version": "2021b"}
+# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results.
+# Disabling vectorize was confirmed to fix the the known issues.
+# With no test suite, sticking to known working toolchain options until proven otherwise.
+toolchainopts = {"cstd": "c++11", "vectorize": False}
+
+source_urls = ["https://bitbucket.org/lesituu/libwallmodelledles/get/"]
+sources = ["af3c659d16d54238364e8812ae8fbe3e46f5e656.tar.gz"]
+checksums = ["06b2c06ef76b5247c0a0c0260ea1e4a58bed8e930d0a0add9fe60e626c4bc0f8"]
+
+dependencies = [
+    ("OpenFOAM", "v2112"),
+]
+
+extract_sources = True
+
+install_cmd = "source $FOAM_BASH && "
+
+# variables of target install directory
+install_cmd += "export WM_PROJECT_USER_DIR=%(installdir)s && "
+install_cmd += "export FOAM_USER_APPBIN=%(installdir)s/bin && "
+install_cmd += "export FOAM_USER_LIBBIN=%(installdir)s/lib && "
+install_cmd += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && "
+
+install_cmd += "pwd && ls && ./Allwmake -j %(parallel)s "
+install_cmd += " && cp -av tests %(installdir)s "
+
+sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLES.so"]}
+sanity_check_commands = [
+    "source $FOAM_BASH && cd %(installdir)s/test/testCases/channel_flow && pimpleFoam"
+]
+# modloadmsg = "Please run 'source $FOAM_BASH' before using RheoTool."
+
+
+moduleclass = "cae"

From bc015f7ab372355d5623b97ee5d3206564a2bff1 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Wed, 8 Mar 2023 11:52:07 +0100
Subject: [PATCH 072/601] Removed copied comment.

---
 .../l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
index cf48519506d..3650fc58eb9 100644
--- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
@@ -39,7 +39,5 @@ sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLE
 sanity_check_commands = [
     "source $FOAM_BASH && cd %(installdir)s/test/testCases/channel_flow && pimpleFoam"
 ]
-# modloadmsg = "Please run 'source $FOAM_BASH' before using RheoTool."
-
 
 moduleclass = "cae"

From c0ba619453dffb0d2ec713c3a25925f0f62ad026 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Wed, 8 Mar 2023 12:09:12 +0100
Subject: [PATCH 073/601] Fixed tests.

---
 .../l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
index 3650fc58eb9..0efcf31e2cf 100644
--- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
@@ -37,7 +37,7 @@ install_cmd += " && cp -av tests %(installdir)s "
 
 sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLES.so"]}
 sanity_check_commands = [
-    "source $FOAM_BASH && cd %(installdir)s/test/testCases/channel_flow && pimpleFoam"
+    "source $FOAM_BASH && cd %(installdir)s/tests/testCases/channel_flow && pimpleFoam"
 ]
 
 moduleclass = "cae"

From 8a9f2ac1c725754588036017bb54c738d5fe6a3c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 11 Mar 2023 00:05:31 +0100
Subject: [PATCH 074/601] adding easyconfigs: CellOracle-0.12.0-foss-2022a.eb,
 GimmeMotifs-0.17.2-foss-2022a.eb, qnorm-0.8.1-foss-2022a.eb,
 Qtconsole-5.4.0-GCCcore-11.3.0.eb

---
 .../CellOracle-0.12.0-foss-2022a.eb           | 59 ++++++++++++++
 .../GimmeMotifs-0.17.2-foss-2022a.eb          | 77 +++++++++++++++++++
 .../Qtconsole-5.4.0-GCCcore-11.3.0.eb         | 31 ++++++++
 .../q/qnorm/qnorm-0.8.1-foss-2022a.eb         | 36 +++++++++
 4 files changed, 203 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb
new file mode 100644
index 00000000000..e712870108d
--- /dev/null
+++ b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb
@@ -0,0 +1,59 @@
+easyblock = 'PythonBundle'
+
+name = 'CellOracle'
+version = '0.12.0'
+
+homepage = 'https://github.com/morris-lab/CellOracle'
+description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data
+and Gene Regulatory Network models."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('R', '4.2.1'),
+    ('SciPy-bundle', '2022.05'),
+    ('numba', '0.56.4'),
+    ('matplotlib', '3.5.2'),
+    ('Seaborn', '0.12.1'),
+    ('scikit-learn', '1.1.2'),
+    ('h5py', '3.7.0'),
+    ('velocyto', '0.17.17'),
+    ('umap-learn', '0.5.3'),
+    ('Arrow', '8.0.0'),
+    ('tqdm', '4.64.0'),
+    ('igraph', '0.10.3'),
+    ('IPython', '8.5.0'),
+    ('scanpy', '1.9.1'),
+    ('GOATOOLS', '1.3.1'),
+    ('genomepy', '0.15.0'),
+    ('GimmeMotifs', '0.17.2'),
+    ('Qtconsole', '5.4.0'),
+]
+
+use_pip = True
+
+# remove louvain from requirements, since CellOracle doesn't actually use it at all
+local_preinstallopts = "sed -i '/louvain/d' requirements.txt && "
+# drop strict version requirement for gimmemotifs dependency
+local_preinstallopts += "sed -i 's/gimmemotifs.*/gimmemotifs/g' requirements.txt && "
+
+exts_list = [
+    ('jupyter-console', '6.4.4', {
+        'sources': ['jupyter_console-%(version)s.tar.gz'],
+        'checksums': ['172f5335e31d600df61613a97b7f0352f2c8250bbd1092ef2d658f77249f89fb'],
+    }),
+    ('jupyter', '1.0.0', {
+        'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'],
+    }),
+    ('celloracle', version, {
+        'checksums': ['9d533ee3e8c14828b6859ea195e92d184b050b0782fee430eda3b01359a564d5'],
+        'preinstallopts': local_preinstallopts,
+    }),
+]
+
+sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb
new file mode 100644
index 00000000000..a57ae34779f
--- /dev/null
+++ b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb
@@ -0,0 +1,77 @@
+easyblock = 'PythonBundle'
+
+name = 'GimmeMotifs'
+version = '0.17.2'
+
+homepage = 'https://github.com/vanheeringen-lab/gimmemotifs'
+description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+    ('pybedtools', '0.9.0'),
+    ('Pysam', '0.19.1'),
+    ('scikit-learn', '1.1.2'),
+    ('Seaborn', '0.12.1'),
+    ('statsmodels', '0.13.1'),
+    ('tqdm', '4.64.0'),
+    ('genomepy', '0.15.0'),
+    ('qnorm', '0.8.1'),
+    ('Arrow', '8.0.0'),  # provides pyarrow, required by feather-format
+    ('HTSeq', '2.0.2'),  # required by biofluff
+    ('pyBigWig', '0.3.18'),  # required by biofluff
+]
+
+use_pip = True
+
+exts_list = [
+    ('palettable', '3.3.0', {
+        'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'],
+    }),
+    ('biofluff', '3.0.4', {
+        'modulename': 'fluff',
+        'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'],
+    }),
+    ('diskcache', '5.4.0', {
+        'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'],
+    }),
+    ('feather-format', '0.4.1', {
+        'modulename': 'feather',
+        'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'],
+    }),
+    ('iteround', '1.0.4', {
+        'source_urls': ['https://github.com/cgdeboer/iteround/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'],
+    }),
+    ('logomaker', '0.8', {
+        'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'],
+    }),
+    ('loguru', '0.6.0', {
+        'checksums': ['066bd06758d0a513e9836fd9c6b5a75bfb3fd36841f4b996bc60b547a309d41c'],
+    }),
+    ('xxhash', '3.2.0', {
+        'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'],
+    }),
+    ('xdg', '6.0.0', {
+        'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'],
+    }),
+    ('gimmemotifs', version, {
+        'preinstallopts': """sed -i '/"configparser"/d' setup.py && """,
+        'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gimme'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["gimme --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..4ca3e9f8a2e
--- /dev/null
+++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'Qtconsole'
+version = '5.4.0'
+
+homepage = 'https://jupyter.org/'
+description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media 
+output, session export, and more.
+The Qtconsole is a very lightweight application that largely feels like a       
+terminal, but provides a number of enhancements only possible in a GUI, such as 
+inline figures, proper multiline editing with syntax highlighting, graphical    
+calltips, and more."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['57748ea2fd26320a0b77adba20131cfbb13818c7c96d83fafcb110ff55f58b35']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('IPython', '8.5.0'),
+    ('QtPy', '2.3.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb
new file mode 100644
index 00000000000..1b0932b22af
--- /dev/null
+++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonPackage'
+
+name = 'qnorm'
+version = '0.8.1'
+
+homepage = 'https://github.com/Maarten-vd-Sande/qnorm'
+description = "Fast-ish (and correct!) quantile normalization in Python"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('numba', '0.56.4'),
+]
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7']
+
+download_dep_fail = True
+use_pip = True
+
+# pyproject.toml included in qnorm source tarball does not include standard fields,
+# it's only there to be read by setup.py...
+preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && "
+
+sanity_check_paths = {
+    'files': ['bin/qnorm'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["qnorm --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 6eb15435bbe4fd3307d7a8a75141cddb38c49c12 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Tue, 14 Mar 2023 08:00:52 +0100
Subject: [PATCH 075/601] adding easyconfigs:
 CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb, pytest-7.2.2-GCCcore-11.2.0.eb

---
 .../CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb     | 59 +++++++++++++++
 .../p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb   | 71 +++++++++++++++++++
 2 files changed, 130 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
 create mode 100644 easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
new file mode 100644
index 00000000000..62fd8a72ed5
--- /dev/null
+++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
@@ -0,0 +1,59 @@
+easyblock = 'PythonBundle'
+
+name = 'CuPy'
+version = '11.4.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://cupy.dev'
+description = "CuPy is an open-source array library accelerated with NVIDIA CUDA."
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+builddependencies = [
+    ('pytest', '7.2.2'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),
+    ('CUDA', '11.4.1', '', SYSTEM),
+    ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM),
+    ('NCCL', '2.10.3', versionsuffix),
+    ('cuTENSOR', '1.6.1.5', versionsuffix, SYSTEM),
+    # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]}
+
+# A bunch of the tests are failing or are just having problems.
+_skip_tests = [
+    'tests/cupyx_tests/scipy_tests',
+    'tests/cupyx_tests/distributed_tests',
+    'tests/cupyx_tests/tools_tests',
+    'tests/example_tests',
+    'tests/cupy_tests/testing_tests/test_parameterized.py',
+    'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_',
+    'tests/cupy_tests/fft_tests/test_fft.py',
+]
+_ignore_list = ' --ignore='.join(_skip_tests)
+
+exts_list = [
+    ('fastrlock', '0.5', {
+        'checksums': ['9ae1a31f6e069b5f0f28ba63c594d0c952065de0a375f7b491d21ebaccc5166f'],
+    }),
+    ('cupy', version, {
+        'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=tests/cupyx_tests/scipy_tests --ignore=tests/cupyx_tests/distributed_tests --ignore=tests/cupyx_tests/tools_tests --ignore=tests/example_tests --ignore=tests/cupy_tests/testing_tests/test_parameterized.py --ignore=tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_ --ignore=tests/cupy_tests/fft_tests/test_fft.py tests",
+        'testinstall': True,
+        'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import cupy'",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
new file mode 100644
index 00000000000..7a10fc0c9b0
--- /dev/null
+++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
@@ -0,0 +1,71 @@
+easyblock = 'PythonBundle'
+
+name = 'pytest'
+version = '7.2.2'
+
+homepage = 'https://docs.pytest.org/en/latest/'
+description = """The pytest framework makes it easy to write small,
+readable tests, and can scale to support complex functional testing for
+applications and libraries."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+dependencies = [
+    ('binutils', '2.37'),
+    ('Python', '3.9.6'),
+]
+
+use_pip = True
+
+exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]}
+
+_skip_tests = [
+    'testing/io/test_terminalwriter.py',
+    'testing/test_terminal.py',
+    'testing/test_debugging.py',
+    'testing/test_config.py',
+    'testing/test_helpconfig.py',
+]
+_ignore_tests = ' --ignore='.join(_skip_tests)
+
+exts_list = [
+    ('tomli', '2.0.1', {
+        'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'],
+    }),
+    ('setuptools-scm', '7.1.0', {
+        'source_tmpl': 'setuptools_scm-%(version)s.tar.gz',
+        'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'],
+    }),
+    ('flit-core', '3.8.0', {
+        'source_tmpl': 'flit_core-%(version)s.tar.gz',
+        'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'],
+    }),
+    ('flit-scm', '1.7.0', {
+        'source_tmpl': 'flit_scm-%(version)s.tar.gz',
+        'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'],
+    }),
+    ('exceptiongroup', '1.1.0', {
+        'checksums': ['bcb67d800a4497e1b404c2dd44fca47d3b7a5e5433dbab67f96c1a685cdfdf23'],
+    }),
+    ('hypothesis', '6.54.6', {
+        'checksums': ['2d5e2d5ccd0efce4e0968a6164f4e4853f808e33f4d91490c975c98beec0c7c3'],
+    }),
+    ('elementpath', '4.0.1', {
+        'checksums': ['1162e4c8e5501bd36291b668f4449b8125fea5ef64a26da8d71da31126725aa5'],
+    }),
+    ('xmlschema', '2.2.2', {
+        'checksums': ['0caa96668807b4b51c42a0fe2b6610752bc59f069615df3e34dcfffb962973fd'],
+    }),
+    (name, version, {
+        'checksums': ['c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'import pytest'",
+    'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' % _ignore_tests,
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From cc94864a2a48ad4a2952fd1baddff1a4a9e7a787 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Tue, 14 Mar 2023 08:22:36 +0100
Subject: [PATCH 076/601] Fix too long lines.

---
 .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb  | 4 +++-
 easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 3 ++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
index 62fd8a72ed5..5108d852855 100644
--- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
@@ -44,7 +44,9 @@ exts_list = [
         'checksums': ['9ae1a31f6e069b5f0f28ba63c594d0c952065de0a375f7b491d21ebaccc5166f'],
     }),
     ('cupy', version, {
-        'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=tests/cupyx_tests/scipy_tests --ignore=tests/cupyx_tests/distributed_tests --ignore=tests/cupyx_tests/tools_tests --ignore=tests/example_tests --ignore=tests/cupy_tests/testing_tests/test_parameterized.py --ignore=tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_ --ignore=tests/cupy_tests/fft_tests/test_fft.py tests",
+        # Must run tests here since the required version of pytest is a builddep
+        # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory.
+        'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=%s tests" % _ignore_list,
         'testinstall': True,
         'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'],
     }),
diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
index 7a10fc0c9b0..34d5c8cdb7e 100644
--- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
@@ -63,7 +63,8 @@ exts_list = [
 
 sanity_check_commands = [
     "python -c 'import pytest'",
-    'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' % _ignore_tests,
+    'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing'
+    % _ignore_tests,
 ]
 
 sanity_pip_check = True

From 76ddb33fd7d4851f046c87f8d4b192b562dc7a25 Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Tue, 14 Mar 2023 13:27:56 +0100
Subject: [PATCH 077/601] Added easyconfig for Apache Avro C++

---
 .../a/avrocpp-1.11.1-GCC-11.2.0.eb            | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb
new file mode 100644
index 00000000000..2bb4e395f6a
--- /dev/null
+++ b/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'Binary'
+
+name = 'avrocpp'
+version = '1.11.1'
+
+homepage = 'https://avro.apache.org/docs/1.11.1/api/cpp/html/'
+description = """Avro C++ is a C++ data serialization library ."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/apache/avro/archive/refs/tags/']
+sources = ['release-%(version)s.tar.gz']
+checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752']
+
+builddependencies = [
+    ('binutils', '2.37', '', ('GCCcore', '11.2.0')),
+    ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')),
+]
+dependencies = [
+    ('Boost', '1.77.0'),
+]
+
+
+extract_sources = True
+
+install_cmd = "cd lang/c++; mkdir -p build; cd build && "
+install_cmd += ' cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=%(installdir)s/ -DCMAKE_BUILD_TYPE=Release .. && '
+install_cmd += "  make install"
+
+
+sanity_check_paths = {
+    'files': ["%(installdir)s/bin/avrogencpp"],
+    'dirs': ["%(installdir)s/lib"],
+}
+
+sanity_check_commands = ["%(installdir)s/bin/avrogencpp -h"]
+
+moduleclass = 'lib'

From ffafbcfe7be5f97f40d91bd306ddb56606d1d7c1 Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Tue, 14 Mar 2023 13:50:20 +0100
Subject: [PATCH 078/601] Added easyconfig for Apache Avro C++

---
 .../easyconfigs/a/{ => avrocpp}/avrocpp-1.11.1-GCC-11.2.0.eb      | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/a/{ => avrocpp}/avrocpp-1.11.1-GCC-11.2.0.eb (100%)

diff --git a/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb
similarity index 100%
rename from easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb
rename to easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb

From c7212533ce2140348fe1abe0e53300782de373b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 14 Mar 2023 19:42:11 +0100
Subject: [PATCH 079/601] Update
 easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb

---
 .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
index 5108d852855..a665a1371c4 100644
--- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
@@ -46,7 +46,8 @@ exts_list = [
     ('cupy', version, {
         # Must run tests here since the required version of pytest is a builddep
         # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory.
-        'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=%s tests" % _ignore_list,
+        'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' %\
+                   _ignore_list,
         'testinstall': True,
         'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'],
     }),

From 9a9e7d06e891c6f224345a193821de9304cd6dac Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 15 Mar 2023 07:53:58 +0100
Subject: [PATCH 080/601] pytest does not need binutils as dependency

---
 easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
index 34d5c8cdb7e..c0f51325944 100644
--- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
@@ -11,7 +11,6 @@ applications and libraries."""
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
 dependencies = [
-    ('binutils', '2.37'),
     ('Python', '3.9.6'),
 ]
 

From a9075126ae999d2a6ac8f32a79fdbc1f7b5d15f2 Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Wed, 15 Mar 2023 09:53:54 +0100
Subject: [PATCH 081/601] Modified easyconfig for Apache Avro C++. Using
 CMakeMake EasyBlock now.

---
 .../a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb       | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb
index 2bb4e395f6a..cbfe03410d3 100644
--- a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb
@@ -1,10 +1,10 @@
-easyblock = 'Binary'
+easyblock = 'CMakeMake'
 
 name = 'avrocpp'
 version = '1.11.1'
 
-homepage = 'https://avro.apache.org/docs/1.11.1/api/cpp/html/'
-description = """Avro C++ is a C++ data serialization library ."""
+homepage = 'https://avro.apache.org'
+description = """Avro is a data serialization system."""
 
 toolchain = {'name': 'GCC', 'version': '11.2.0'}
 
@@ -20,13 +20,13 @@ dependencies = [
     ('Boost', '1.77.0'),
 ]
 
+srcdir = "%(builddir)s/avro-release-%(version)s/lang/c++"
 
-extract_sources = True
-
-install_cmd = "cd lang/c++; mkdir -p build; cd build && "
-install_cmd += ' cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=%(installdir)s/ -DCMAKE_BUILD_TYPE=Release .. && '
-install_cmd += "  make install"
+generator = "Unix Makefiles"
+separate_build_dir = True
 
+configopts = ' -DCMAKE_INSTALL_PREFIX=%(installdir)s/'
+configopts += ' -DCMAKE_BUILD_TYPE=Release '
 
 sanity_check_paths = {
     'files': ["%(installdir)s/bin/avrogencpp"],

From 15dfe73200ba85ba58bd9f58e3279148b5d878a9 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 15 Mar 2023 11:37:39 +0100
Subject: [PATCH 082/601] pytest does need binutils as an explicit builddep
 since it is in GCCcore according to our rules.

---
 easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
index c0f51325944..e8ab8e89799 100644
--- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
@@ -10,6 +10,10 @@ applications and libraries."""
 
 toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
+builddependencies = [
+    ('binutils', '2.37'),
+]
+
 dependencies = [
     ('Python', '3.9.6'),
 ]

From 9e91f4d4194611ca38265ea759ecde904c93afed Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Mar 2023 16:25:41 +0100
Subject: [PATCH 083/601] bump tcsh to 6.24.07, use foss/2022b for WRF 4.4.1,
 add easyconfig for netCDF 4.6.0 with gompi/2022b

---
 .../netCDF-Fortran-4.6.0-gompi-2022b.eb       | 28 +++++++++++++++++++
 ....2.0.eb => tcsh-6.24.07-GCCcore-12.2.0.eb} |  4 +--
 ...dmpar.eb => WRF-4.4.1-foss-2022b-dmpar.eb} |  4 +--
 3 files changed, 32 insertions(+), 4 deletions(-)
 create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb
 rename easybuild/easyconfigs/t/tcsh/{tcsh-6.24.05-GCCcore-12.2.0.eb => tcsh-6.24.07-GCCcore-12.2.0.eb} (93%)
 rename easybuild/easyconfigs/w/WRF/{WRF-4.4.1-foss-2022.10-dmpar.eb => WRF-4.4.1-foss-2022b-dmpar.eb} (94%)

diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb
new file mode 100644
index 00000000000..e7d505dc509
--- /dev/null
+++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb
@@ -0,0 +1,28 @@
+name = 'netCDF-Fortran'
+version = '4.6.0'
+
+homepage = 'https://www.unidata.ucar.edu/software/netcdf/'
+description = """NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data."""
+
+toolchain = {'name': 'gompi', 'version': '2022b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca']
+
+builddependencies = [
+    ('M4', '1.4.19'),
+]
+
+dependencies = [
+    ('netCDF', '4.9.0'),
+    ('bzip2', '1.0.8'),
+]
+
+# (too) parallel build fails, but single-core build is fairly quick anyway (~1min)
+parallel = 1
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb
similarity index 93%
rename from easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb
rename to easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb
index 5874f3e8c14..f2a441e8129 100644
--- a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb
@@ -12,7 +12,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'tcsh'
-version = '6.24.05'
+version = '6.24.07'
 
 homepage = 'https://www.tcsh.org'
 description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh).
@@ -29,7 +29,7 @@ source_urls = [
     'ftp://ftp.astron.com/pub/%(namelower)s/old',
 ]
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['3d1ff94787859b5a4063400470251618f76bc24f8041ba7ef2c2753f782c296c']
+checksums = ['74e4e9805cbd9413ed34b4ffa1d72fc8d0ef81a5b79476854091416ce9336995']
 
 builddependencies = [('binutils', '2.39')]
 
diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb
similarity index 94%
rename from easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb
rename to easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb
index 95e02318341..a62a23d620c 100644
--- a/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb
+++ b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb
@@ -8,7 +8,7 @@ description = """The Weather Research and Forecasting (WRF) Model is a next-gene
  numerical weather prediction system designed to serve both operational forecasting and atmospheric
  research needs."""
 
-toolchain = {'name': 'foss', 'version': '2022.10'}
+toolchain = {'name': 'foss', 'version': '2022b'}
 toolchainopts = {'opt': False}  # don't use agressive optimization, stick to -O2
 
 source_urls = ['https://github.com/wrf-model/WRF/archive/']
@@ -34,7 +34,7 @@ checksums = [
 # csh is used by WRF install scripts
 builddependencies = [
     ('Autotools', '20220317'),
-    ('tcsh', '6.24.05'),
+    ('tcsh', '6.24.07'),
     ('time', '1.9'),
     ('Perl', '5.36.0'),
 ]

From 170a69fbe0d7f27b8be212733f9acc4842b917fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 15 Mar 2023 17:55:17 +0000
Subject: [PATCH 084/601] adding easyconfigs:
 PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb

---
 ...ch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..6d6afd348d6
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,57 @@
+easyblock = 'PythonBundle'
+
+name = 'PyTorch-bundle'
+version = '1.12.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://pytorch.org/'
+description = """PyTorch with compatible versions of official Torch extensions."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('RE2', '2022-06-01'),  # for torchtext
+]
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('PyTorch', version, versionsuffix),
+    ('Pillow-SIMD', '9.2.0'),  # for torchvision
+    ('SentencePiece', '0.1.97'),  # for torchtext
+    ('tqdm', '4.64.0'),  # for torchtext
+    ('double-conversion', '3.2.0'),  # for torchtext
+]
+
+use_pip = True
+
+exts_list = [
+    ('torchvision', '0.14.1', {
+        'source_urls': ['https://github.com/pytorch/vision/archive'],
+        'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'],
+    }),
+    ('torchtext', '0.14.1', {
+        'source_urls': ['https://github.com/pytorch/text/archive'],
+        'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'],
+    }),
+    ('torchaudio', '0.13.1', {
+        'source_urls': ['https://github.com/pytorch/audio/archive'],
+        'sources': [{'download_filename': 'v0.13.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['3a5c108a9ea31d0e6533a2cd6cbaf133efaefe4bdcb4b689183a33b991c95d12'],
+    }),
+    ('pytorch-ignite', '0.4.11', {
+        'source_urls': ['https://github.com/pytorch/ignite/archive'],
+        'sources': [{'download_filename': 'v0.4.11.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'],
+    }),
+    ('torchdata', '0.6.0', {
+        'source_urls': ['https://github.com/pytorch/data/archive'],
+        'sources': [{'download_filename': 'v0.6.0.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['048dea12ee96c0ea1525097959fee811d7b38c2ed05f44a90f35f8961895fb5b'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'

From d81414e5b1b08320152c7759e80c78a0695cb399 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 15 Mar 2023 18:49:57 +0000
Subject: [PATCH 085/601] Fix version template in download filename

---
 .../PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
index 6d6afd348d6..00e581f3322 100644
--- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -27,27 +27,27 @@ use_pip = True
 exts_list = [
     ('torchvision', '0.14.1', {
         'source_urls': ['https://github.com/pytorch/vision/archive'],
-        'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'],
     }),
     ('torchtext', '0.14.1', {
         'source_urls': ['https://github.com/pytorch/text/archive'],
-        'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'sources': [{'download_filename': 'v%(version)S.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'],
     }),
     ('torchaudio', '0.13.1', {
         'source_urls': ['https://github.com/pytorch/audio/archive'],
-        'sources': [{'download_filename': 'v0.13.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['3a5c108a9ea31d0e6533a2cd6cbaf133efaefe4bdcb4b689183a33b991c95d12'],
     }),
     ('pytorch-ignite', '0.4.11', {
         'source_urls': ['https://github.com/pytorch/ignite/archive'],
-        'sources': [{'download_filename': 'v0.4.11.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'],
     }),
     ('torchdata', '0.6.0', {
         'source_urls': ['https://github.com/pytorch/data/archive'],
-        'sources': [{'download_filename': 'v0.6.0.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['048dea12ee96c0ea1525097959fee811d7b38c2ed05f44a90f35f8961895fb5b'],
     }),
 ]

From 930088708b580d743b62f7c9e337869136e579a9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 15 Mar 2023 21:52:15 +0100
Subject: [PATCH 086/601] adding easyconfigs: MATLAB-2022b-r5.eb

---
 .../easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb   | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb

diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb
new file mode 100644
index 00000000000..4ffbc980772
--- /dev/null
+++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb
@@ -0,0 +1,28 @@
+name = 'MATLAB'
+version = '2022b'
+_update = '5'
+versionsuffix = '-r%s' % _update
+
+homepage = 'https://www.mathworks.com/products/matlab'
+description = """MATLAB is a high-level language and interactive environment
+ that enables you to perform computationally intensive tasks faster than with
+ traditional programming languages such as C, C++, and Fortran."""
+
+toolchain = SYSTEM
+
+sources = ['R%s_Update_%s_Linux.iso' % (version, _update)]
+checksums = ['d11ba428a6970208f0855138a6e2253c31e2ead34d51da125529a208945ac187']
+
+java_options = '-Xmx2048m'
+
+osdependencies = [('p7zip-plugins', 'p7zip-full')]  # for extracting iso-files
+
+# Use EB_MATLAB_KEY environment variable or uncomment and modify license key
+# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000'
+
+# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or
+# uncomment and modify the following variables for installation with floating license server
+# license_file = 'my-license-file'
+# license_server_port = 'XXXXX'
+
+moduleclass = 'math'

From 558cf0452a8cefce9de1ef2c7d3a675bc8e64c38 Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Thu, 16 Mar 2023 09:34:07 +0100
Subject: [PATCH 087/601] easyconfig changes implemented and name changed to
 avro-cpp.

---
 .../avro-cpp-1.11.1-GCC-11.2.0.eb}               | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)
 rename easybuild/easyconfigs/a/{avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb => avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb} (56%)

diff --git a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb
similarity index 56%
rename from easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb
rename to easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb
index cbfe03410d3..58138a0d9c3 100644
--- a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb
@@ -1,10 +1,10 @@
 easyblock = 'CMakeMake'
 
-name = 'avrocpp'
+name = 'avro-cpp'
 version = '1.11.1'
 
 homepage = 'https://avro.apache.org'
-description = """Avro is a data serialization system."""
+description = """C++ implementation of Avro data serialization system."""
 
 toolchain = {'name': 'GCC', 'version': '11.2.0'}
 
@@ -13,8 +13,7 @@ sources = ['release-%(version)s.tar.gz']
 checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752']
 
 builddependencies = [
-    ('binutils', '2.37', '', ('GCCcore', '11.2.0')),
-    ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')),
+    ('CMake', '3.22.1'),
 ]
 dependencies = [
     ('Boost', '1.77.0'),
@@ -25,14 +24,11 @@ srcdir = "%(builddir)s/avro-release-%(version)s/lang/c++"
 generator = "Unix Makefiles"
 separate_build_dir = True
 
-configopts = ' -DCMAKE_INSTALL_PREFIX=%(installdir)s/'
-configopts += ' -DCMAKE_BUILD_TYPE=Release '
-
 sanity_check_paths = {
-    'files': ["%(installdir)s/bin/avrogencpp"],
-    'dirs': ["%(installdir)s/lib"],
+    'files': ["bin/avrogencpp"],
+    'dirs': ["lib"],
 }
 
-sanity_check_commands = ["%(installdir)s/bin/avrogencpp -h"]
+sanity_check_commands = ["avrogencpp -h"]
 
 moduleclass = 'lib'

From b41bc9c17d3d0697dd3abf723d78c99c23a612cf Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Thu, 16 Mar 2023 09:52:37 +0100
Subject: [PATCH 088/601] srcdir path changed

---
 easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb
index 58138a0d9c3..8ef5d09f68e 100644
--- a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb
@@ -19,7 +19,7 @@ dependencies = [
     ('Boost', '1.77.0'),
 ]
 
-srcdir = "%(builddir)s/avro-release-%(version)s/lang/c++"
+srcdir = "lang/c++"
 
 generator = "Unix Makefiles"
 separate_build_dir = True

From b3e0ccaf8340c1ef3681b31d1bd50a1980e3b0d7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 16 Mar 2023 09:56:34 +0000
Subject: [PATCH 089/601] fix typo

---
 .../PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
index 00e581f3322..89b09adbe87 100644
--- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -32,7 +32,7 @@ exts_list = [
     }),
     ('torchtext', '0.14.1', {
         'source_urls': ['https://github.com/pytorch/text/archive'],
-        'sources': [{'download_filename': 'v%(version)S.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'],
     }),
     ('torchaudio', '0.13.1', {

From 191d7ff6be89ec1f822dd68503b228364cad6692 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 16 Mar 2023 11:03:57 +0100
Subject: [PATCH 090/601] adding easyconfigs:
 torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb and patches:
 torchtext-0.14.1_deps_fix.patch

---
 ...chtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb | 46 ++++++++++++++++
 .../torchtext/torchtext-0.14.1_deps_fix.patch | 53 +++++++++++++++++++
 2 files changed, 99 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
 create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
new file mode 100644
index 00000000000..46bf098eddc
--- /dev/null
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
@@ -0,0 +1,46 @@
+easyblock = 'PythonPackage'
+
+name = 'torchtext'
+version = '0.14.1'
+local_pytorch_version = '1.12.0'
+local_python_suffix = '-Python-%(pyver)s'
+versionsuffix = '-PyTorch-%s' % local_pytorch_version
+
+homepage = 'https://github.com/pytorch/text'
+description = "Data loaders and abstractions for text and NLP"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# Sources are no longer available in PyPI, it only has wheels
+source_urls = ['https://github.com/pytorch/text/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['torchtext-0.14.1_deps_fix.patch']
+checksums = [
+    {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
+    {'torchtext-0.14.1_deps_fix.patch': '38ee9a2c74016376ef3ff06ea40eb4522f5a72410573168050b79cab457077c7'},
+]
+
+builddependencies = [
+    ('RE2', '2022-06-01'),
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('SentencePiece', '0.1.97'),
+    ('tqdm', '4.64.0'),
+    ('PyTorch', local_pytorch_version),
+    ('double-conversion', '3.2.0'),
+    ('utf8proc', '2.7.0'),
+]
+
+download_dep_fail = True,
+use_pip = True
+sanity_pip_check = True,
+
+# Disable bundled libraries to use those from EB: RE2, SentencePiece
+preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && "
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch
new file mode 100644
index 00000000000..ab7a71f24f5
--- /dev/null
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch
@@ -0,0 +1,53 @@
+diff -u text/CMakeLists.txt.orig text/CMakeLists.txt
+--- text/CMakeLists.txt.orig	2023-03-08 14:33:35.618931003 +0100
++++ text/CMakeLists.txt	2023-03-08 14:35:03.169072623 +0100
+@@ -24,10 +24,10 @@
+ if(env_cxx_standard GREATER -1)
+   message(
+       WARNING "C++ standard version definition detected in environment variable."
+-      "PyTorch requires -std=c++14. Please remove -std=c++ settings in your environment.")
++      "PyTorch requires -std=c++17. Please remove -std=c++ settings in your environment.")
+ endif()
+
+-set(CMAKE_CXX_STANDARD 14)
++set(CMAKE_CXX_STANDARD 17)
+ set(CMAKE_C_STANDARD 11)
+
+ set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+@@ -63,5 +63,10 @@
+
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_COMPILED_WITH_CXX_ABI} -Wall ${TORCH_CXX_FLAGS}")
+
+-add_subdirectory(third_party)
++find_package(double-conversion)
++find_package(re2)
++find_library(SENTENCEPIECE_LIBRARY sentencepiece PATHS $ENV{EBROOTSENTENCEPIECE}/lib64)
++find_library(SENTENCEPIECE_TRAIN_LIBRARY sentencepiece_train PATHS $ENV{EBROOTSENTENCEPIECE}/lib64)
++find_library(UTF8PROC_LIBRARY utf8proc PATHS $ENV{UTF8PROC}/lib64)
++
+ add_subdirectory(torchtext/csrc)
+diff -u text/torchtext/csrc/CMakeLists.txt.orig text/torchtext/csrc/CMakeLists.txt
+--- text/torchtext/csrc/CMakeLists.txt.orig 2023-03-08 14:11:53.387582628 +0100
++++ text/torchtext/csrc/CMakeLists.txt      2023-03-08 14:16:11.159140070 +0100
+@@ -18,10 +18,6 @@
+ set(
+   LIBTORCHTEXT_INCLUDE_DIRS
+   ${PROJECT_SOURCE_DIR}
+-  ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src
+-  $<TARGET_PROPERTY:re2,INCLUDE_DIRECTORIES>
+-  $<TARGET_PROPERTY:double-conversion,INCLUDE_DIRECTORIES>
+-  $<TARGET_PROPERTY:utf8proc,INCLUDE_DIRECTORIES>
+   ${TORCH_INSTALL_PREFIX}/include
+   ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include
+   )
+@@ -119,10 +115,6 @@
+   set(
+     EXTENSION_INCLUDE_DIRS
+     ${PROJECT_SOURCE_DIR}
+-    ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src
+-    $<TARGET_PROPERTY:re2,INCLUDE_DIRECTORIES>
+-    $<TARGET_PROPERTY:double-conversion,INCLUDE_DIRECTORIES>
+-    $<TARGET_PROPERTY:utf8proc,INCLUDE_DIRECTORIES>
+     ${TORCH_INSTALL_PREFIX}/include
+     ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include
+     )

From a9c11959b36418d54c376354781c459101977837 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Mar 2023 16:12:15 +0100
Subject: [PATCH 091/601] adding easyconfigs: PIPITS-3.0-foss-2022a.eb,
 ITSx-1.1.3-GCCcore-11.3.0.eb, FASTX-Toolkit-0.0.14-GCC-11.3.0.eb

---
 .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb        | 74 +++++++++++++++++++
 .../i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb       | 29 ++++++++
 .../p/PIPITS/PIPITS-3.0-foss-2022a.eb         | 66 +++++++++++++++++
 3 files changed, 169 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
new file mode 100644
index 00000000000..4bde8e513e1
--- /dev/null
+++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
@@ -0,0 +1,74 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
+easyblock = 'Bundle'
+
+name = 'FASTX-Toolkit'
+version = '0.0.14'
+
+homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/'
+description = """The FASTX-Toolkit is a collection of command line tools for 
+ Short-Reads FASTA/FASTQ files preprocessing."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+default_easyblock = 'ConfigureMake'
+
+dependencies = [('GDGraph', '1.56')]
+
+components = [
+    ('libgtextutils', '0.7', {
+        'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'],
+        'sources': [SOURCE_TAR_GZ],
+        'patches': ['libgtextutils-%(version)s_fix-bool.patch'],
+        'checksums': [
+            '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a',  # libgtextutils-0.7.tar.gz
+            'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00',  # libgtextutils-0.7_fix-bool.patch
+        ],
+        'start_dir': 'libgtextutils-%(version)s',
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'],
+        'sources': ['fastx_toolkit-%(version)s.tar.bz2'],
+        'checksums': ['9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806'],
+        'start_dir': 'fastx_toolkit-%(version)s',
+        'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ",
+        'configopts': 'CXXFLAGS="$CXXFLAGS -Wno-implicit-fallthrough"',
+    }),
+]
+
+sanity_check_paths = {
+    'files':
+        ['bin/fastx_%s' % x for x in
+            ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement',
+             'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh',
+             'nucleotide_distribution_line_graph.sh']] +
+        ['bin/fasta_%s' % x for x in
+            ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] +
+        ['bin/fastq_%s' % x for x in
+            ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter',
+             'quality_trimmer', 'masker']] +
+        ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    'fasta_clipping_histogram.pl',
+    'fasta_formatter -h',
+    'fastq_masker -h | grep "FASTX Toolkit %(version)s"',
+    'fastq_quality_boxplot_graph.sh',
+    'fastx_clipper -h | grep "FASTX Toolkit %(version)s"',
+    'fastx_nucleotide_distribution_graph.sh',
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..7392f5fd08a
--- /dev/null
+++ b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'Tarball'
+
+name = 'ITSx'
+version = '1.1.3'
+
+homepage = 'https://microbiology.se/software/itsx/'
+description = '''ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of
+fungi and other eukaryotes for use in environmental sequencing.'''
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://microbiology.se/sw/']
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['6f6d7ff6350f82439dee5348f6e8bda512be25193c603d4e56cc215c520091bf']
+
+dependencies = [('Perl', '5.34.1')]
+
+fix_perl_shebang_for = ['ITSx']
+
+sanity_check_paths = {
+    'files': ['ITSx'],
+    'dirs': ['ITSx_db'],
+}
+
+sanity_check_commands = ['ITSx --help']
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb
new file mode 100644
index 00000000000..561a7f5e9c2
--- /dev/null
+++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb
@@ -0,0 +1,66 @@
+easyblock = 'PythonBundle'
+
+name = 'PIPITS'
+version = '3.0'
+
+homepage = 'https://github.com/hsgweon/pipits'
+description = """An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences 
+from the Illumina sequencing platform."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('h5py', '3.7.0'),
+    ('VSEARCH', '2.22.1'),
+    ('FASTX-Toolkit', '0.0.14'),
+    ('ITSx', '1.1.3'),
+    ('HMMER', '3.3.2'),
+    ('RDP-Classifier', '2.13', '-Java-11', SYSTEM),
+    ('SeqKit', '2.3.1', '', SYSTEM),
+]
+
+use_pip = True
+
+exts_list = [
+    ('biom-format', '2.1.14', {
+        'modulename': 'biom',
+        'checksums': ['c8bac94ab6aa8226c0d38af7a3341d65e5f3664b9f45ec44fdf8b5275b2f92c1'],
+    }),
+    ('python-utils', '3.5.2', {
+        'checksums': ['68198854fc276bc4b2403b261703c218e01ef564dcb072a7096ed9ea7aa5130c'],
+    }),
+    ('progressbar2', '4.2.0', {
+        'modulename': 'progressbar',
+        'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'],
+    }),
+    ('pispino', '1.1', {
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/hsgweon/pispino/archive/'],
+        'checksums': ['8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0'],
+    }),
+    (name, version, {
+        'patches': ['PIPITS-3.0_remove-conda-commands.patch'],
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/hsgweon/pipits/archive/'],
+        'checksums': [
+            {'3.0.tar.gz': 'ee9f142e473e57b186760d940131610c16bdfe57eefca935df35779fd85377bd'},
+            {'PIPITS-3.0_remove-conda-commands.patch':
+             'd4be41ac4d6d37a19ad09b06c1f05ed83921aa59dc4b04b38fa257e6bce6d12f'},
+        ],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['pipits_funits', 'pipits_process',
+                                     'pispino_createreadpairslist',
+                                     'pispino_seqprep']],
+    'dirs': []
+}
+
+sanity_check_commands = ['pipits_process --help']
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From a7d7295aa25e5809350d5b9dbae1def75672b1fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Mar 2023 16:40:55 +0100
Subject: [PATCH 092/601] fix the perl shebangs

---
 .../f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb          | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
index 4bde8e513e1..d249cdca076 100644
--- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
@@ -47,6 +47,8 @@ components = [
     }),
 ]
 
+fix_perl_shebang_for = ['bin/*.pl']
+
 sanity_check_paths = {
     'files':
         ['bin/fastx_%s' % x for x in

From 009e515103443fa7c61f7d8435213c3ac88372d5 Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Thu, 16 Mar 2023 16:50:15 +0100
Subject: [PATCH 093/601] Avro c++ with GCCcore toolchain

---
 .../avro-cpp-1.11.1-GCCcore-11.2.0.eb         | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb
new file mode 100644
index 00000000000..17e21b86b52
--- /dev/null
+++ b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'CMakeMake'
+
+name = 'avro-cpp'
+version = '1.11.1'
+
+homepage = 'https://avro.apache.org'
+description = """C++ implementation of Avro data serialization system."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/apache/avro/archive/refs/tags/']
+sources = ['release-%(version)s.tar.gz']
+checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752']
+
+builddependencies = [
+    ('binutils', '2.37'),
+    ('CMake', '3.22.1'),
+]
+
+dependencies = [
+    ('Boost', '1.77.0', '', ('GCC', '11.2.0')),
+]
+
+srcdir = "lang/c++"
+
+generator = "Unix Makefiles"
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ["bin/avrogencpp"],
+    'dirs': ["lib"],
+}
+
+sanity_check_commands = ["avrogencpp -h"]
+
+moduleclass = 'lib'

From 652c494b7f51b826835028c563963225e7bd8ea6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Mar 2023 17:04:55 +0100
Subject: [PATCH 094/601] add dep on Perl, add ext PerlIO::gzip, add another
 sanity check cmd

---
 .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb          | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
index d249cdca076..652930a60f8 100644
--- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
@@ -24,7 +24,10 @@ toolchainopts = {'pic': True}
 
 default_easyblock = 'ConfigureMake'
 
-dependencies = [('GDGraph', '1.56')]
+dependencies = [
+    ('GDGraph', '1.56'),
+     ('Perl', '5.34.1'),
+]
 
 components = [
     ('libgtextutils', '0.7', {
@@ -47,6 +50,17 @@ components = [
     }),
 ]
 
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('PerlIO::gzip', '0.20', {
+        'source_tmpl': 'PerlIO-gzip-0.20.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'],
+        'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'],
+    }),
+]
+
 fix_perl_shebang_for = ['bin/*.pl']
 
 sanity_check_paths = {
@@ -69,6 +83,7 @@ sanity_check_commands = [
     'fasta_formatter -h',
     'fastq_masker -h | grep "FASTX Toolkit %(version)s"',
     'fastq_quality_boxplot_graph.sh',
+    'fastx_barcode_splitter.pl --help | grep "Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008"',
     'fastx_clipper -h | grep "FASTX Toolkit %(version)s"',
     'fastx_nucleotide_distribution_graph.sh',
 ]

From 304f0825ac14c75de5f69f8bd2b8740aff117315 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Mar 2023 17:08:24 +0100
Subject: [PATCH 095/601] Also need to set PERL5LIB

---
 .../f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb        | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
index 652930a60f8..7b16b587b3e 100644
--- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
@@ -63,6 +63,10 @@ exts_list = [
 
 fix_perl_shebang_for = ['bin/*.pl']
 
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'
+}
+
 sanity_check_paths = {
     'files':
         ['bin/fastx_%s' % x for x in

From d725f608971e073b76e392703056aa9bb6c1d94e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 16 Mar 2023 17:29:17 +0100
Subject: [PATCH 096/601] Fix indentation

---
 .../f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
index 7b16b587b3e..8589f7ecedc 100644
--- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
@@ -26,7 +26,7 @@ default_easyblock = 'ConfigureMake'
 
 dependencies = [
     ('GDGraph', '1.56'),
-     ('Perl', '5.34.1'),
+    ('Perl', '5.34.1'),
 ]
 
 components = [

From 74a7c591091b1d4c385f74c2f9f0580888d5de06 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 16 Mar 2023 23:05:07 +0100
Subject: [PATCH 097/601] {phys}[foss/2022b] TOPAS v3.9, CLHEP v2.4.6.4, GDCM
 v3.0.21

---
 .../c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb       | 27 ++++++++++
 .../g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb      | 28 ++++++++++
 .../t/TOPAS/TOPAS-3.9-foss-2022b.eb           | 54 +++++++++++++++++++
 3 files changed, 109 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb

diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb
new file mode 100644
index 00000000000..1a08a4ed224
--- /dev/null
+++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'CMakeMake'
+
+name = 'CLHEP'
+version = '2.4.6.4'
+
+homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/'
+description = """The CLHEP project is intended to be a set of HEP-specific foundation and
+ utility classes such as random generators, physics vectors, geometry and linear algebra.
+ CLHEP is structured in a set of packages independent of any external package."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/']
+sources = [SOURCELOWER_TGZ]
+checksums = ['49c89330f1903ef707d3c5d79c16a7c5a6f2c90fc290e2034ee3834809489e57']
+
+builddependencies = [('CMake', '3.24.3')]
+
+sanity_check_paths = {
+    'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT],
+    'dirs': ['include/CLHEP'],
+}
+
+sanity_check_commands = ["clhep-config --help"]
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..298041d52e0
--- /dev/null
+++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'GDCM'
+version = '3.0.21'
+
+homepage = 'https://sourceforge.net/projects/gdcm'
+description = "Grassroots DICOM: Cross-platform DICOM implementation"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['f29dbdd3b6b4c30c9803e6466b88b139d67f5585768565fe29f0be65ad737744']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0"
+
+sanity_check_paths = {
+    'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'],
+    'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb b/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb
new file mode 100644
index 00000000000..294567fbc07
--- /dev/null
+++ b/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb
@@ -0,0 +1,54 @@
+easyblock = 'Bundle'
+
+name = 'TOPAS'
+version = '3.9'
+
+homepage = 'https://www.topasmc.org'
+description = """TOPAS wraps and extends the Geant4 Simulation Toolkit to make advanced Monte Carlo simulation of all
+forms of radiotherapy easier to use for medical physicists."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('expat', '2.4.9'),
+    ('X11', '20221110'),
+    ('Mesa', '22.2.4'),
+    ('libGLU', '9.0.2'),
+    ('Qt5', '5.15.7'),
+    ('HarfBuzz', '5.3.1'),
+    ('GDCM', '3.0.21'),
+    ('CLHEP', '2.4.6.4'),
+]
+
+local_geant4_configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include"
+local_geant4_configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF -DGEANT4_BUILD_MULTITHREADED=ON "
+
+components = [
+    # TOPAS required Geant4 10.x, which must be built with multi-threading support
+    ('Geant4', '10.7.4', {
+        'github_account': 'Geant4',
+        'source_urls': [GITHUB_SOURCE],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}],
+        'checksums': ['602b41dfee1fa6b33b026d00c5bd940155d7e5d0b3495230a87e2a25b28f9996'],
+        'start_dir': 'geant4-%(version)s',
+        'configopts': local_geant4_configopts,
+    }),
+    (name, version, {
+        'easyblock': 'CMakeMake',
+        'download_instructions': "Manual download required, see https://www.topasmc.org/download",
+        'sources': ['topas_%(version_major)s_%(version_minor)s.zip'],
+        'checksums': ['57739f8df5fe58f47b2cc5ac646b4776ab137d52640c6e5b1f6cd199ed3c7b0f'],
+        'start_dir': 'topas_%(version_major)s_%(version_minor)s',
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/topas', 'lib/libchemistry.a', 'lib/libG4run.%s' % SHLIB_EXT, 'lib/libmain.a', 'lib/libphysics.a'],
+    'dirs': ['examples', 'include'],
+}
+
+moduleclass = 'phys'

From 4111f711dfca1c970c9618e612b59766a94db32c Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 17 Mar 2023 08:29:32 +0100
Subject: [PATCH 098/601] adding easyconfigs: M3GNet-0.2.4-foss-2022a.eb,
 pymatgen-2023.3.10-foss-2022a.eb

---
 .../m/M3GNet/M3GNet-0.2.4-foss-2022a.eb       | 42 ++++++++++
 .../pymatgen/pymatgen-2023.3.10-foss-2022a.eb | 81 +++++++++++++++++++
 2 files changed, 123 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb

diff --git a/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb
new file mode 100644
index 00000000000..65f7885f206
--- /dev/null
+++ b/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'M3GNet'
+version = '0.2.4'
+
+homepage = 'https://materialsvirtuallab.github.io/m3gnet/'
+description = """"
+M3GNet is a new materials graph neural network architecture that incorporates
+3-body interactions. A key difference with prior materials graph
+implementations such as MEGNet is the addition of the coordinates for atoms and
+the 3×3 lattice matrix in crystals, which are necessary for obtaining tensorial
+quantities such as forces and stresses via auto-differentiation.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('ASE', '3.22.1'),
+    ('TensorFlow', '2.11.0'),
+    ('pymatgen', '2023.3.10'),
+    ('h5py', '3.7.0'),  # optional, for model saving
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
+        'checksums': ['a7f82b06f48d8fb81f91fb88484177005066cdf708902bf749afaa7f8d117ce8'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/m3g'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/m3gnet'],
+}
+
+sanity_check_commands = ['m3g --help']
+
+moduleclass = 'phys'
diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb
new file mode 100644
index 00000000000..1adc774c4b6
--- /dev/null
+++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb
@@ -0,0 +1,81 @@
+easyblock = 'PythonBundle'
+
+name = 'pymatgen'
+version = '2023.3.10'
+
+homepage = 'https://pymatgen.org/'
+description = """Python Materials Genomics is a robust materials analysis code that defines core object
+ representations for structures and molecules with support for many electronic structure codes."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('hypothesis', '6.46.7'),  # required for numpy tests
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('PyYAML', '6.0'),
+    ('matplotlib', '3.5.2'),
+    ('networkx', '2.8.4'),
+    ('sympy', '1.11.1'),
+    ('plotly.py', '5.12.0'),
+    ('tqdm', '4.64.0'),
+
+]
+
+use_pip = True
+
+# pymatgen 2023.3.10 requires spglib >= 2.0.2
+# skip import check for ruamel.yaml.clib, covered by import check for ruamel.yaml extension
+exts_list = [
+    ('monty', '2022.9.9', {
+        'checksums': ['6cca8f14a18a2030b243a1377dfd59049a1ccce007b34f810a8f5eece72b9ceb'],
+    }),
+    ('palettable', '3.3.0', {
+        'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'],
+    }),
+    ('ruamel.yaml.clib', '0.2.7', {
+        'modulename': False,
+        'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'],
+    }),
+    ('ruamel.yaml', '0.17.21', {
+        'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'],
+    }),
+    ('uncertainties', '3.1.7', {
+        'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'],
+    }),
+    ('latexcodec', '2.0.1', {
+        'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'],
+    }),
+    ('pybtex', '0.24.0', {
+        'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'],
+    }),
+    ('pydantic', '1.10.2', {
+        'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'],
+    }),
+    ('emmet-core', '0.49.1', {
+        'modulename': 'emmet',
+        'checksums': ['8133d63900c170ac5c66efe8d70c32c9762c9a42fc150a79c7c90a8477ac81ec'],
+    }),
+    ('mp-api', '0.30.10', {
+        'checksums': ['b58522b106f362d6917eba97ef8d699cc87210b65a9f0a8ac70c0841110ce50a'],
+    }),
+    ('spglib', '2.0.2', {
+        'checksums': ['1d081ec22da4ab4fc3198e9445ddad6dec2261c43927831151d93e39422610aa'],
+    }),
+    (name, version, {
+        'checksums': ['20a5d1681e2951d2710d5358197b5b58992e2b0ec4217a5ba966cf28513c1283'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/pmg'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["pmg --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'chem'

From d42c60d64dd94a11f9f4b5786de56e969858c12f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 17 Mar 2023 10:37:58 +0000
Subject: [PATCH 099/601] Switch to torchdata 0.5.1

---
 .../PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb         | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
index 89b09adbe87..62ab4bc5ff8 100644
--- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -31,6 +31,8 @@ exts_list = [
         'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'],
     }),
     ('torchtext', '0.14.1', {
+        # Disable bundled libraries to use those from EB: RE2, SentencePiece
+        'preinstallopts': "sed -i '/third_party/d;/BuildExtension/d' setup.py &&",
         'source_urls': ['https://github.com/pytorch/text/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'],
@@ -45,10 +47,10 @@ exts_list = [
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'],
     }),
-    ('torchdata', '0.6.0', {
+    ('torchdata', '0.5.1', {
         'source_urls': ['https://github.com/pytorch/data/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['048dea12ee96c0ea1525097959fee811d7b38c2ed05f44a90f35f8961895fb5b'],
+        'checksums': ['69d80bd33ce8f08e7cfeeb71cefddfc29cede25a85881e33dbae47576b96ed29'],
     }),
 ]
 

From 5af7bc9f581ce7030480c7238b7e6a734b8de6dc Mon Sep 17 00:00:00 2001
From: Steven Vandenbrande <steven.vandenbrande@kuleuven.be>
Date: Fri, 17 Mar 2023 17:44:42 +0100
Subject: [PATCH 100/601] Disable qopt report in GraphBLAS compilation

---
 .../SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb  |  8 +++++++-
 .../SuiteSparse_disable-qopt-report.patch          | 14 ++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
index d896b7962de..5b48dcf1cb2 100644
--- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
@@ -11,7 +11,13 @@ toolchainopts = {'unroll': True, 'pic': True}
 
 source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
 sources = ['v%(version)s.tar.gz']
-checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee']
+patches = [
+    'SuiteSparse_disable-qopt-report.patch',
+]
+checksums = [
+    {'v5.10.1.tar.gz': 'acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'},
+    {'SuiteSparse_disable-qopt-report.patch': 'f96bcd993f4dd90a70aedcb2901582ac99f449ac359b46a36190862a16aeb870'},
+]
 
 builddependencies = [
     ('CMake', '3.20.1'),
diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch
new file mode 100644
index 00000000000..db00fb87ea1
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch
@@ -0,0 +1,14 @@
+Compiling GraphBLAS with the intel toolchain consumes *a lot* of memory
+because optimization reports are generated. This patch simply turns that off
+to make the memory requirement for compilation more sensible.
+--- GraphBLAS/CMakeLists.txt.orig	2023-03-17 14:46:24.533943000 +0100
++++ GraphBLAS/CMakeLists.txt	2023-03-17 14:46:15.393912000 +0100
+@@ -198,7 +198,7 @@
+ elseif ( "${CMAKE_C_COMPILER_ID}" STREQUAL "Intel" )
+     # options for icc: also needs -std=c11
+     set ( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -diag-disable 10397,15552 " )
+-    set ( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -qopt-report=5 -qopt-report-phase=vec" )
++    set ( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -qopt-report=0 -qopt-report-phase=vec" )
+     # the -mp1 option is important for predictable floating-point results with
+     # the icc compiler.  Without, ((float) 1.)/((float) 0.) produces NaN,
+     # instead of the correct result, Inf.

From 5f2dd890807b9b70758c70260998a2a2ae4c5912 Mon Sep 17 00:00:00 2001
From: Steven Vandenbrande <steven.vandenbrande@kuleuven.be>
Date: Fri, 17 Mar 2023 17:46:13 +0100
Subject: [PATCH 101/601] Use JOBS variable to set make parallelism

---
 .../SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
index 5b48dcf1cb2..810a3aa16d0 100644
--- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb
@@ -31,5 +31,9 @@ dependencies = [
 
 # make sure that bin/demo can find libsuitesparseconfig.so.5 during build
 prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
+# The default way to do a parallel make won't work with the Makefiles for
+# SuiteSparse, JOBS has to be set to the desired parallelism
+parallel = 1
+prebuildopts += "export JOBS=4 && "
 
 moduleclass = 'numlib'

From 64bd3e60b1a14291ddef33ad7f5869fc0d4ed0e8 Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Sat, 18 Mar 2023 10:46:39 +0100
Subject: [PATCH 102/601] adding easyconfigs: ASE-3.22.1-foss-2022b.eb,
 Flask-2.2.3-GCCcore-12.2.0.eb, spglib-python-2.0.2-gfbf-2022b.eb

---
 .../a/ASE/ASE-3.22.1-foss-2022b.eb            | 63 +++++++++++++++++++
 .../f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb     | 55 ++++++++++++++++
 .../spglib-python-2.0.2-gfbf-2022b.eb         | 27 ++++++++
 3 files changed, 145 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb

diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb
new file mode 100644
index 00000000000..4a076fc342b
--- /dev/null
+++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb
@@ -0,0 +1,63 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.22.1'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language.
+
+From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations
+in C of functions in ASE.  ASE uses it automatically when installed."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('Flask', '2.2.3'),
+    ('matplotlib', '3.7.0'),
+    ('Tkinter', '%(pyver)s'),     # Needed by GUI of ASE
+    ('spglib-python', '2.0.2'),  # optional
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pytest-mock', '3.8.2', {
+        'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'],
+    }),
+    ('ase', version, {
+        'patches': [
+            'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch',
+            'ASE-3.22.1-Compatibility-with-pytest-part-2.patch',
+            'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch',
+            'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch',
+        ],
+        'checksums': [
+            '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432',  # ase-3.22.1.tar.gz
+            # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch
+            '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac',
+            # ASE-3.22.1-Compatibility-with-pytest-part-2.patch
+            '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601',
+            # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch
+            'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8',
+            # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch
+            '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d',
+        ],
+    }),
+    ('ase-ext', '20.9.0', {
+        'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..26e22ef4b44
--- /dev/null
+++ b/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb
@@ -0,0 +1,55 @@
+easyblock = 'PythonBundle'
+
+name = 'Flask'
+version = '2.2.3'
+
+homepage = 'https://www.palletsprojects.com/p/flask/'
+description = """
+Flask is a lightweight WSGI web application framework. It is designed to make
+getting started quick and easy, with the ability to scale up to complex
+applications.
+This module includes the Flask extensions: Flask-Cors"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+builddependencies = [('binutils', '2.39')]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('itsdangerous', '2.1.2', {
+        'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'],
+    }),
+    ('Werkzeug', version, {
+        'checksums': ['2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe'],
+    }),
+    ('asgiref', '3.6.0', {
+        'checksums': ['9567dfe7bd8d3c8c892227827c41cce860b368104c3431da67a0c5a65a949506'],
+    }),
+    (name, version, {
+        'checksums': ['7eb373984bf1c770023fce9db164ed0c3353cd0b53f130f4693da0ca756a2e6d'],
+    }),
+    ('Flask-Cors', '3.0.10', {
+        'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'],
+    }),
+    ('cachelib', '0.10.2', {
+        'checksums': ['593faeee62a7c037d50fc835617a01b887503f972fb52b188ae7e50e9cb69740'],
+    }),
+    ('Flask-Session', '0.4.0', {
+        'checksums': ['c9ed54321fa8c4ca0132ffd3369582759eda7252fb4b3bee480e690d1ba41f46'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/flask'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['flask --version']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb
new file mode 100644
index 00000000000..76b88995143
--- /dev/null
+++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'spglib-python'
+version = '2.0.2'
+
+homepage = 'https://pypi.python.org/pypi/spglib'
+description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C."
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib']
+sources = ['spglib-%(version)s.tar.gz']
+checksums = ['1d081ec22da4ab4fc3198e9445ddad6dec2261c43927831151d93e39422610aa']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+options = {'modulename': 'spglib'}
+
+moduleclass = 'chem'

From c94dbda543ece1fcd7a938c8eb55400e1ed34bbe Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Sat, 18 Mar 2023 13:20:11 +0100
Subject: [PATCH 103/601] adding easyconfigs: networkx-2.8.8-gfbf-2022b.eb

---
 .../n/networkx/networkx-2.8.8-gfbf-2022b.eb   | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb

diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb
new file mode 100644
index 00000000000..bac13dc9e35
--- /dev/null
+++ b/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'networkx'
+version = '2.8.8'
+
+homepage = 'https://pypi.python.org/pypi/networkx'
+description = """NetworkX is a Python package for the creation, manipulation,
+and study of the structure, dynamics, and functions of complex networks."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['230d388117af870fce5647a3c52401fcf753e94720e6ea6b4197a5355648885e']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),  # required for numpy, scipy, ...
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'

From ce3732ae91a27e3d9a8705afd235d157637e809f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 18 Mar 2023 14:47:19 +0100
Subject: [PATCH 104/601] adding easyconfigs: MDAnalysis-2.4.2-foss-2021a.eb

---
 .../MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb

diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb
new file mode 100644
index 00000000000..e5f35ff61b3
--- /dev/null
+++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb
@@ -0,0 +1,57 @@
+easyblock = 'PythonBundle'
+
+name = 'MDAnalysis'
+version = '2.4.2'
+
+homepage = 'https://www.mdanalysis.org/'
+description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD)
+simulations in many popular formats."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('matplotlib', '3.4.2'),
+    ('networkx', '2.5.1'),
+    ('tqdm', '4.61.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('mrcfile', '1.4.3', {
+        'checksums': ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'],
+    }),
+    ('GridDataFormats', '1.0.1', {
+        'modulename': 'gridData',
+        'checksums': ['ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4'],
+    }),
+    ('gsd', '2.8.0', {
+        'checksums': ['f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae'],
+    }),
+    ('msgpack', '1.0.5', {
+        'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'],
+    }),
+    ('mmtf-python', '1.1.3', {
+        'modulename': 'mmtf',
+        'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'],
+    }),
+    ('fasteners', '0.18', {
+        'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'],
+    }),
+    # MDAnalysis 2.4.x requires biopython >= 1.80
+    ('biopython', '1.81', {
+        'checksums': ['2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0'],
+        'runtest': "python setup.py test --offline",
+        'modulename': 'Bio',
+        'sanity_check_commands': ["python -c 'import Bio.MarkovModel'"],
+    }),
+    (name, version, {
+        'modulename': 'MDAnalysis',
+        'checksums': ['ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636'],
+    }),
+]
+
+moduleclass = 'bio'

From 645a6b0a54705e5b642b9df8507e78f9d01dce55 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Sat, 18 Mar 2023 16:19:10 +0100
Subject: [PATCH 105/601] downgrade sympy version

---
 .../easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb
index 1adc774c4b6..bc8ccfc43a9 100644
--- a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb
@@ -18,7 +18,7 @@ dependencies = [
     ('PyYAML', '6.0'),
     ('matplotlib', '3.5.2'),
     ('networkx', '2.8.4'),
-    ('sympy', '1.11.1'),
+    ('sympy', '1.10.1'),
     ('plotly.py', '5.12.0'),
     ('tqdm', '4.64.0'),
 

From 9daef5988231d3c3f96f0308d84fe6028da6bad1 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 18 Mar 2023 15:50:56 +0000
Subject: [PATCH 106/601] adding easyconfigs:
 RapidJSON-1.1.0-GCCcore-12.2.0.eb, RE2-2023-03-01-GCCcore-12.2.0.eb,
 utf8proc-2.8.0-GCCcore-12.2.0.eb

---
 .../r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb    | 33 +++++++++++++++++++
 .../RapidJSON-1.1.0-GCCcore-12.2.0.eb         | 30 +++++++++++++++++
 .../utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb | 30 +++++++++++++++++
 3 files changed, 93 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..b43aca00751
--- /dev/null
+++ b/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb
@@ -0,0 +1,33 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+easyblock = "CMakeMake"
+
+name = 'RE2'
+version = '2023-03-01'
+
+homepage = 'https://github.com/google/re2'
+description = """
+RE2 is a fast, safe, thread-friendly alternative to backtracking regular
+expression engines like those used in PCRE, Perl, and Python. It is a C++
+library. """
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'google'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['7a9a4824958586980926a300b4717202485c4b4115ac031822e29aa4ef207e48']
+
+builddependencies = {
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+}
+
+sanity_check_paths = {
+    'files': ['lib/libre2.a'],
+    'dirs': ['include/re2'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..9594b13fd9d
--- /dev/null
+++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'RapidJSON'
+version = '1.1.0'
+
+homepage = 'https://rapidjson.org'
+description = "A fast JSON parser/generator for C++ with both SAX/DOM style API"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/Tencent/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_fix-compiler-errors.patch']
+checksums = [
+    'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e',  # v1.1.0.tar.gz
+    # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch
+    '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7',
+]
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/pkgconfig/%(name)s.pc'],
+    'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..33d5c5ec66a
--- /dev/null
+++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'utf8proc'
+version = '2.8.0'
+
+homepage = 'https://github.com/JuliaStrings/utf8proc'
+description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, 
+and other operations for data in the UTF-8 encoding."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a0a60a79fe6f6d54e7d411facbfcc867a6e198608f2cd992490e46f04b1bcecc']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+separate_build_dir = True
+
+configopts = ['', '-DBUILD_SHARED_LIBS=true']
+
+sanity_check_paths = {
+    'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From c4b2e3cc6d6198e6e9d215f7232f1bb7829df1bb Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 18 Mar 2023 15:51:31 +0000
Subject: [PATCH 107/601] adding easyconfigs: Arrow-11.0.0-gfbf-2022b.eb,
 arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb

---
 .../a/Arrow/Arrow-11.0.0-gfbf-2022b.eb        | 73 +++++++++++++++++++
 .../arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb    | 34 +++++++++
 2 files changed, 107 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb
 create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb

diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb
new file mode 100644
index 00000000000..d35cad0f1b3
--- /dev/null
+++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb
@@ -0,0 +1,73 @@
+easyblock = 'CMakeMake'
+
+name = 'Arrow'
+version = '11.0.0'
+
+homepage = 'https://arrow.apache.org'
+description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform
+ for in-memory data."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s']
+sources = ['apache-arrow-%(version)s.tar.gz']
+checksums = ['2dd8f0ea0848a58785628ee3a57675548d509e17213a2f5d72b0d900b43f5430']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Autotools', '20220317'),
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    ('pkgconf', '1.9.3'),
+]
+
+# Arrow strongly prefers included jemalloc, so not including it as a dependency
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),  # for numpy
+    ('Boost', '1.81.0'),
+    ('lz4', '1.9.4'),
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('zstd', '1.5.2'),
+    ('snappy', '1.1.9'),
+    ('RapidJSON', '1.1.0'),
+    ('RE2', '2023-03-01'),
+    ('utf8proc', '2.8.0'),
+]
+
+start_dir = 'cpp'
+
+# see https://arrow.apache.org/docs/developers/python.html
+configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON "
+configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON "
+configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON "
+configopts += "-DZSTD_ROOT=$EBROOTZSTD "
+
+# also install Python bindings
+local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && "
+local_install_pyarrow_cmds += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && "
+local_install_pyarrow_cmds += "export Parquet_DIR=%(installdir)s && "
+local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && "
+local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && "
+local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && "
+local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON "
+local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT
+local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ."
+postinstallcmds = [local_install_pyarrow_cmds]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT,
+              'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT],
+    'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "python -c 'import pyarrow'",
+    "python -c 'import pyarrow.dataset'",
+    "python -c 'import pyarrow.parquet'",
+]
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb
new file mode 100644
index 00000000000..dfe97712e3b
--- /dev/null
+++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb
@@ -0,0 +1,34 @@
+easyblock = 'RPackage'
+
+name = 'arrow-R'
+version = '11.0.0.3'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://cran.r-project.org/web/packages/arrow'
+description = "R interface to the Apache Arrow C++ library"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/Archive/arrow',  # package archive
+    'https://cran.r-project.org/src/contrib/',  # current version of packages
+    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+]
+sources = ['arrow_%(version)s.tar.gz']
+checksums = ['eb939471f5f4218e6cfd62f58ccd2a0a5283d4a19a2902741c7fb25e2f016eaf']
+
+dependencies = [
+    ('R', '4.2.2'),
+    ('Arrow', '11.0.0'),
+]
+
+preinstallopts = "export LIBARROW_BINARY=true && "
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['arrow'],
+}
+
+options = {'modulename': 'arrow'}
+
+moduleclass = 'tools'

From a0de2c20a6384d940ba7bd15c9caf0d2e6eafe8d Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 18 Mar 2023 16:57:01 +0000
Subject: [PATCH 108/601] adding easyconfigs:
 R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

---
 ...le-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 1240 +++++++++++++++++
 1 file changed, 1240 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
new file mode 100644
index 00000000000..352ea582005
--- /dev/null
+++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
@@ -0,0 +1,1240 @@
+easyblock = 'Bundle'
+
+name = 'R-bundle-Bioconductor'
+version = '3.16'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://bioconductor.org'
+description = """Bioconductor provides tools for the analysis and coprehension
+ of high-throughput genomic data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+# lpsymphony fails to build with pkgconf, so stick to pkg-config
+# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286
+# builddependencies = [('pkg-config', '0.29.2')]
+builddependencies = [('pkgconf', '1.9.3')]
+
+dependencies = [
+    ('R', '4.2.2'),
+    ('Boost', '1.81.0'),  # for mzR
+    ('GSL', '2.7'),  # for flowClust
+    ('HDF5', '1.14.0'),  # for rhdf5
+    ('arrow-R', '11.0.0.3', versionsuffix),  # required by RcisTarget
+]
+
+exts_default_options = {
+    'source_urls': [
+        'https://bioconductor.org/packages/3.16/bioc/src/contrib/',
+        'https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/%(name)s',
+        'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/',
+        'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/',
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz'
+}
+
+exts_defaultclass = 'RPackage'
+
+# check whether correct version is installed in extension filter
+# (some versions in this bundle may be newer than the ones provided by R)
+local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') "
+local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')"
+exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg))
+
+# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends
+# !! order of packages is important !!
+# packages updated on 7th Nov 2022
+exts_list = [
+    ('BiocGenerics', '0.44.0', {
+        'checksums': ['8518e462c1ef103ab059d059d871afc444e48f56fe6b3afdb60dc1abf6c9b09d'],
+    }),
+    ('Biobase', '2.58.0', {
+        'checksums': ['db798af54eb18d83242b1ffbb1fa35b5bc0256cedf86b9a6519e2d786d20e566'],
+    }),
+    ('S4Vectors', '0.36.2', {
+        'checksums': ['68b441289882bde641a1d736287b2dfb837c21b21e18b127b9fee1fc5d792c8c'],
+    }),
+    ('IRanges', '2.32.0', {
+        'checksums': ['097935916b5cb33804e1ea09fa6c4ee7ddeaa03eef99138a05b1896b28dc6a4b'],
+    }),
+    ('GenomeInfoDbData', '1.2.9', {
+        'checksums': ['e63a719a8eceefeda39fc95de83e7aa41caad39705efc712a44ab4021adc45fa'],
+    }),
+    ('GenomeInfoDb', '1.34.9', {
+        'checksums': ['2bbb094636bf628447ed4c49b4cd96c164264d012a59f0fe5982f12e6a6bc956'],
+    }),
+    ('zlibbioc', '1.44.0', {
+        'checksums': ['8b2616b722e2d610cdd41aba1a94b987ab017e0bfff63f6ce66f191e81abe530'],
+    }),
+    ('XVector', '0.38.0', {
+        'checksums': ['e9ba0ec3f4124c6f0ce13c4d562e7e4419f8aa5db4283092574a63a207f4ed79'],
+    }),
+    ('Biostrings', '2.66.0', {
+        'checksums': ['7312c508bc2fe6ea3da75edd621b41a35929f9dbdca16d25eb3724ca2cd206fd'],
+    }),
+    ('KEGGREST', '1.38.0', {
+        'checksums': ['ec9fe4b9e11858ba1236c22c9058ea3b3e6967168c847b01003b15d1afb94318'],
+    }),
+    ('AnnotationDbi', '1.60.2', {
+        'checksums': ['0f52a460cefc40919273463648656c306640cf82afee3bd0fd2941dbde16eeb0'],
+    }),
+    ('GenomicRanges', '1.50.2', {
+        'checksums': ['37fdc2074f17b833002c906998b09c88174c054bc5dd9fffdba1f76c4d5d668d'],
+    }),
+    ('BiocParallel', '1.32.5', {
+        'checksums': ['395ed5c19fb706ca73c841c843c3a89f8a88f774a26415bfdbac0dca92a5a6f9'],
+    }),
+    ('Rhtslib', '2.0.0', {
+        'checksums': ['5098bf9f4e8bbbe7eea3d63480c5c970af87b68998d625a2ec0f12b2393727e6'],
+    }),
+    ('Rsamtools', '2.14.0', {
+        'checksums': ['5fe4f80752459f6f1691320ffeffd2d7d17d52dcef60c7a7035fd714ac86a471'],
+    }),
+    ('MatrixGenerics', '1.10.0', {
+        'checksums': ['09fbea178608186571acabc18cd2b81fe5c7aa2d143f5d456ceaed55e01b4815'],
+    }),
+    ('DelayedArray', '0.24.0', {
+        'checksums': ['d764b4f487b49ca04150ea7d8f5f180683cd80575d67a162e4a99cd52bd8815a'],
+    }),
+    ('SummarizedExperiment', '1.28.0', {
+        'checksums': ['96e5e4f496ce32d8c812a7483d9208aa1b89cbf6c0342bd53c95c419bad92721'],
+    }),
+    ('GenomicAlignments', '1.34.1', {
+        'checksums': ['1af0675483cd233ebc4c6d086ffec0c054e0066c424ccea97bc4ec825824e8b0'],
+    }),
+    ('ShortRead', '1.56.1', {
+        'checksums': ['6baea2227937d6458d25dc590ae4d7209efe071fce8d3859e4c97266989476b7'],
+    }),
+    ('graph', '1.76.0', {
+        'checksums': ['8c0ddb6d131a88d585bcf3c1e922465fbc40d6d40ba718c8a869f5f9b6ecabc1'],
+    }),
+    ('affyio', '1.68.0', {
+        'checksums': ['2b3a5fc98ed39b6113031ea989f9cc9271077224cce7d6c83d1a4ef275faacad'],
+    }),
+    ('preprocessCore', '1.60.2', {
+        'installopts': "--configure-args='--disable-threading'",
+        'checksums': ['6d2d5746059a5016e09b3f46f7688de29b5afdf33c6023ce4bc0b7f4eb8c7d46'],
+    }),
+    ('BiocManager', '1.30.20', {
+        'checksums': ['b9e72d7687abbd785a69fecb530ec86ad92257a6be95b8e15953b193a516d5ea'],
+    }),
+    ('affy', '1.76.0', {
+        'checksums': ['f28162f390369957f4bed64c535c64c1901be151c4642cf456065e45704d3dc6'],
+    }),
+    ('GO.db', '3.16.0', {
+        'checksums': ['4652812d8ba380aeeb9b136efbc9365156397eec99c5ca36cfb8294139493b8e'],
+    }),
+    ('limma', '3.54.2', {
+        'checksums': ['0be567ec0e24707ca27bd54d9e86b407e82ffe10fef21ebc4631356a3f1990e1'],
+    }),
+    ('RBGL', '1.74.0', {
+        'checksums': ['35c9808240051d88218514fa69de186f7d64c09b254321a6fc125a67bdee8c35'],
+    }),
+    ('org.Hs.eg.db', '3.16.0', {
+        'checksums': ['2d2e6fdefa0dbb61c86d4736e5a0d430745ae733e310f240b97b2cb3703a2c0a'],
+    }),
+    ('AnnotationForge', '1.40.1', {
+        'checksums': ['de073ce37a6c661696d4de2e577882c7379af49f20181b6be62896660a658d9b'],
+    }),
+    ('annaffy', '1.70.0', {
+        'checksums': ['cf2552152ce81eb209a454efe727bfc913c2f2ef1fddf6dfbe5ac6d32185b163'],
+    }),
+    ('gcrma', '2.70.0', {
+        'checksums': ['c16fc57ae299503aad93cdc7af96cc587f3e7360922cf0de76f54ef924977c28'],
+    }),
+    ('oligoClasses', '1.60.0', {
+        'checksums': ['e8be665b4310a73b1a7f14aefb1949c6fc186eccb7b8522129ee9167baeb69c6'],
+    }),
+    ('edgeR', '3.40.2', {
+        'checksums': ['09f4f4ff636f6bb412c95cda601728151c81c442777636601ba6e132c2224337'],
+    }),
+    ('PFAM.db', '3.16.0', {
+        'checksums': ['8082aaa94eb962b2cf42cfaead8ff9e1bdbd12fdeae82a49d0f3b37bd50eb30c'],
+    }),
+    ('perm', '1.0-0.2', {
+        'checksums': ['729294987bb0f367c67c4bf4071464e097ec9a2bbdb2c63f19ebfb907c604aa0'],
+    }),
+    ('baySeq', '2.31.0', {
+        'checksums': ['900f72debe1aff26cc0232efddf9145592ae5f3317425c938237af38aae30253'],
+    }),
+    ('qvalue', '2.30.0', {
+        'checksums': ['04deeabb43f4f12815cbbe0891b8bfa36abfc82eb2d097b14a28e598585051b7'],
+    }),
+    ('impute', '1.72.3', {
+        'checksums': ['68e8385d04af8bcc6bb69c3a7b3767aa23f0a5856a4f462de6e0cd95d40708e3'],
+    }),
+    ('shinyFiles', '0.9.3', {
+        'checksums': ['4a72e165ee8a6e8256988f27286a2cfc4d7a42e2a902f4f2a728b1c237c07286'],
+    }),
+    ('samr', '3.0', {
+        'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'],
+    }),
+    ('DEGseq', '1.52.0', {
+        'checksums': ['26b3040109926b66598bf3d2a8df186bdbf1fdda62fed1ad4e3ac863ce82a397'],
+    }),
+    ('hgu133plus2.db', '3.13.0', {
+        'checksums': ['ddde58e777a8341536a664c7d4be874a2f395f8aaa019c1f738462a8ce74cc44'],
+    }),
+    ('illuminaio', '0.40.0', {
+        'checksums': ['22f4545c0420ebc42709b7d42562279344eea0c916a734f9fc0c40b8aa1185b3'],
+    }),
+    ('BiocIO', '1.8.0', {
+        'checksums': ['2e41284256ef5dac4deb27ee41f973092e091c387a77cf3e3d588c39aceea495'],
+    }),
+    ('restfulr', '0.0.15', {
+        'checksums': ['40ff8f1fb2987af2223e1a855bb1680c5ce2143fbce7ebc42f1edb291f80e692'],
+    }),
+    ('rtracklayer', '1.58.0', {
+        'checksums': ['b3d2dddd3924ab739324aad65c149949d73d879eeb9e2fe39a6ecd5a9d03b9e3'],
+    }),
+    ('filelock', '1.0.2', {
+        'checksums': ['ac2915950789b16c43a625a2b8dab6ba423588db4a7d0daa75b74518b82b1403'],
+    }),
+    ('BiocFileCache', '2.6.1', {
+        'checksums': ['87a3d98cde0abcdbfa0c8e7a8f77eda78e39be712bc6edefcd85fa778b326198'],
+    }),
+    ('biomaRt', '2.54.0', {
+        'checksums': ['989a1ac3c9f99833c277892dfc868f0aebc8ac106ce4d038766e4d514c7cca30'],
+    }),
+    ('GenomicFeatures', '1.50.4', {
+        'checksums': ['d63cfa59fac2c379b2745263c408b6fe6c9785cb32eb67cbbc450868c72059e3'],
+    }),
+    ('bumphunter', '1.40.0', {
+        'checksums': ['e28d6b3b887b1d83f61d76d4a9c8c2489581b8cd137dc8a92e3c54e844838b4b'],
+    }),
+    ('multtest', '2.54.0', {
+        'checksums': ['e7012d1f04a4aba6b85bef5bbef95c9253408a16c329c4b184a4fe0ba8033f32'],
+    }),
+    ('scrime', '1.3.5', {
+        'checksums': ['5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578'],
+    }),
+    ('siggenes', '1.72.0', {
+        'checksums': ['7bcaf25b8050e72161ef241ba515f74514d31e97dcbfa482519d785334193a3e'],
+    }),
+    ('DynDoc', '1.76.0', {
+        'checksums': ['0bee877511766c478bbbb916fef58c24ad4d347089d9a1436af0da6b4f4a1d71'],
+    }),
+    ('NOISeq', '2.42.0', {
+        'checksums': ['221e4d1396b7c3d412c0f1358a2ea1676c9eabf86ac3f953b27a875ca8531ec8'],
+    }),
+    ('Rgraphviz', '2.42.0', {
+        'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'],
+        'checksums': [
+            {'Rgraphviz_2.42.0.tar.gz': '955b3cff1951725d527f80e51d150e2b0096a0df0f1279a978ff83d055ab9e2e'},
+            {'Rgraphviz-2.28.0_fno-tree-vectorize.patch':
+             '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9'},
+        ],
+    }),
+    ('RNASeqPower', '1.38.0', {
+        'checksums': ['0aad1434beb5d2dfa5329af5d6fae1200e0a2973016ce136901233d5258d12b9'],
+    }),
+    ('annotate', '1.76.0', {
+        'checksums': ['6ad0db66b81c9f998852b18df0cea0847eff3409b71abd03bdc60e6fc6b6551a'],
+    }),
+    ('GSEABase', '1.60.0', {
+        'checksums': ['a583e6286214f10a23f9d385b090f6539a1f7a730a5f327ae23aed6169a40e45'],
+    }),
+    ('genefilter', '1.80.3', {
+        'checksums': ['09995bc8d29311f1083c3f27abbff2e055778666dd9d1941031563d73141f710'],
+    }),
+    ('Category', '2.64.0', {
+        'checksums': ['d0769ce883810e46ce2e464e579cf59221d72e9138a83001ba47accdfc58c2c8'],
+    }),
+    ('GOstats', '2.64.0', {
+        'checksums': ['dadb1b988a81fa24a972ed2f1227c0cda4c425529fe74ced939d5b84a7f3901d'],
+    }),
+    ('BSgenome', '1.66.3', {
+        'checksums': ['46fb92b6bab87c36cdd79f60e1d81c56d02ce06c0ef12e26d21eed9aa2d147df'],
+    }),
+    ('VariantAnnotation', '1.44.1', {
+        'checksums': ['fd430a989ac4c4fcf7f88ee4c0c6e8adc0d086c2a209b1d3e0a569fadaa9f18f'],
+    }),
+    ('interactiveDisplayBase', '1.36.0', {
+        'checksums': ['3fb388572c9250ba2cf56fa56c40adc83c5897ad43b36f219b1c269c44fa4cc8'],
+    }),
+    ('BiocVersion', '3.16.0', {
+        'checksums': ['dc7af08c09242cc436be7b91e46705789d13ac3a3939211ee9be8511fc1057b6'],
+    }),
+    ('AnnotationHub', '3.6.0', {
+        'checksums': ['f6c4062a04a1a8421072ae89cf2ba41ef98c8372cd360f179c89745e0d1660c2'],
+    }),
+    ('AnnotationFilter', '1.22.0', {
+        'checksums': ['d37a0e40e5503c84bc99432c982f4894a10114ae93abe9077074adaeb59b2654'],
+    }),
+    ('ProtGenerics', '1.30.0', {
+        'checksums': ['9116dd55ef2e09f1b1d9d81f4745574d898dcf1d438e58a896357db83e78b7cc'],
+    }),
+    ('ensembldb', '2.22.0', {
+        'checksums': ['51d68978b0f2285be379bbbfbb7b890ac689303434259ef6988a2f5ce3b031ec'],
+    }),
+    ('biovizBase', '1.46.0', {
+        'checksums': ['865393b822d308c96d9987faa0d1e253ad14cf3efd3c3c376896eff2065ea64c'],
+    }),
+    ('OrganismDbi', '1.40.0', {
+        'checksums': ['7cfa7055f5b4625e764ee918e8af46409a7b7f54ad53d3fa4e2268bc38ee8186'],
+    }),
+    ('ggbio', '1.46.0', {
+        'checksums': ['0f983bebac75b2ae957e709d2fa316f547844ceb0136f132e3082ad06df0a3be'],
+    }),
+    ('geneplotter', '1.76.0', {
+        'checksums': ['6a2bf0e14ca16d23c629680967d24c5c08006300483235ee3acceadda6269b24'],
+    }),
+    ('DESeq2', '1.38.3', {
+        'checksums': ['b5db24957eefca903089d9b6ca56db25438a25ad3981ce83fc847eb3647a3e4f'],
+    }),
+    ('ReportingTools', '2.38.0', {
+        'checksums': ['c0673fe479e09590b789ade6d91c50ad7f5e568aa9bc9debf7606301c0b22fdb'],
+    }),
+    ('Glimma', '2.8.0', {
+        'checksums': ['42bcc0390167920fd1b5c58815fcd1beaddaef8aa9aabf315c99f6d1ee5253bb'],
+    }),
+    ('affycoretools', '1.70.0', {
+        'checksums': ['94c4be4223a427763e07bf468e63a1ce2e272a432c5abf4cbd56c2d890a6549f'],
+    }),
+    ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', {
+        'checksums': ['063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9'],
+    }),
+    ('Homo.sapiens', '1.3.1', {
+        'checksums': ['014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94'],
+    }),
+    ('BSgenome.Hsapiens.UCSC.hg19', '1.4.3', {
+        'checksums': ['5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a'],
+    }),
+    ('AgiMicroRna', '2.48.0', {
+        'checksums': ['c7d5319808ec9267e052fecc1336777d3fa8731efe882554801036d2bcf57060'],
+    }),
+    ('geneLenDataBase', '1.34.0', {
+        'checksums': ['8f9cf0b21de1e9042dd8680c86ca93b72f57c0f68d38acf81a0187cdc2d396f5'],
+    }),
+    ('goseq', '1.50.0', {
+        'checksums': ['c8478273cb97f28a827fca7721e31fa51831d467d292a218540c0f4ad0a60975'],
+    }),
+    ('KEGGgraph', '1.58.3', {
+        'checksums': ['c60fd72bdf5f0fd9335779a15f9f299143cab0592406a418dc643274db3fb2e8'],
+    }),
+    ('GEOquery', '2.66.0', {
+        'checksums': ['7602d0cb9c8d600187d599c2fb6d7328f219193c72c4af1987aaf51968556232'],
+    }),
+    ('rARPACK', '0.11-0', {
+        'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'],
+    }),
+    ('mixOmics', '6.22.0', {
+        'checksums': ['3dabec627b5e21da365979d6980565bd338e5a6ec8c3a016f3726ebb6184da70'],
+    }),
+    ('Rhdf5lib', '1.20.0', {
+        'checksums': ['a73b462be309c9df11afc9b941282dcefb36b4a38d15c050fd98bb3c05bbaf7f'],
+    }),
+    ('rhdf5filters', '1.10.0', {
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+    ('motifmatchr', '1.20.0', {
+        'checksums': ['db596cab5ab1292eec380bf2ff6c9b8d7783fc32890935d6574c484bdcb36206'],
+    }),
+    ('extraDistr', '1.9.1', {
+        'checksums': ['9990348c4dbc611684fcb58ab8db7e856dfde1c9c86ffb7705f4b3dff6b2d7bf'],
+    }),
+    ('PRROC', '1.3.1', {
+        'checksums': ['479118ce47c527bc97fb58d531a31cabc094d9843d62f16922009dc62e8248d4'],
+    }),
+    ('TSP', '1.2-3', {
+        'checksums': ['7dfb3cdcbcb79c07eb1db41e66e5e0c872f5f90c7e63eca94afc30bae9cf66b2'],
+    }),
+    ('qap', '0.1-2', {
+        'checksums': ['47a4ada3ae7a3a5c9304174bd5291daad60d329d527c0c6bb5ec1ac257584da5'],
+    }),
+    ('ca', '0.71.1', {
+        'checksums': ['040c2fc94c356075f116cc7cd880530b3c9e02206c0035182c03a525ee99b424'],
+    }),
+    ('seriation', '1.4.2', {
+        'checksums': ['ad19ecbc375aa8121b8a60c6bbd0e7b3a5ab2779dab805c72124caa472ff5090'],
+    }),
+    ('egg', '0.4.5', {
+        'checksums': ['15c8ba7cf2676eb0460de7e5dfbc89fc3175ac22a8869cfd44d66d156fd6c7bb'],
+    }),
+    ('heatmaply', '1.4.2', {
+        'checksums': ['8a92b1ccee11371467f30833255c9ebef2259b6cbdf489181a0adac056c5ea7d'],
+    }),
+    ('OUTRIDER', '1.16.3', {
+        'checksums': ['9684dd78d65e0bbe87e81b6d805824d488179cd96ae4cd351059b522610f6037'],
+    }),
+    ('FRASER', '1.10.2', {
+        'checksums': ['b701286649c2c83fdf8f55ec66f0790d9258e20185464b456e9c79da966b499e'],
+    }),
+    ('JASPAR2020', '0.99.10', {
+        'checksums': ['b9b92d141a317ebb32a14708229f6b82522ceeb5f1b88360d93b0a7cfe30375b'],
+    }),
+    ('AUCell', '1.20.2', {
+        'checksums': ['7a70f12a55a99cfaf1de614469801fffeae21ca0743c2a4dbff9fd5e1a1e61e1'],
+    }),
+    ('RcisTarget', '1.18.2', {
+        'checksums': ['22be06fe8461b2d3f9a0ead86d2126a7c0061e365ad32deb6ec173f845159f0a'],
+    }),
+    ('NMF', '0.25', {
+        'checksums': ['28b918765f6c579c46d9a0638408297df27b78e9c4392abcd1f59e4dbe3fb44d'],
+    }),
+    ('densEstBayes', '1.0-2.1', {
+        'checksums': ['4b7066e18902ee2a0ea084513b237b5fb8e43fe3102354c2fb216d5a8c7df5df'],
+    }),
+    ('reldist', '1.7-2', {
+        'checksums': ['d9086cbc14ed7c65d72da285b86a07e77cbfebc478ba7327b769bd08549229c9'],
+    }),
+    ('M3Drop', '1.24.0', {
+        'checksums': ['66110f22c81144763e38c78c22703cf640924d2953501ec624afda06da111ec1'],
+    }),
+    ('bsseq', '1.34.0', {
+        'checksums': ['4ed397d29efd18fd2de659b72a9e1a137a3c3a16beb82f3cdd334415328ca065'],
+    }),
+    ('DSS', '2.46.0', {
+        'checksums': ['ee494438bf49f33f5cafab56f4b2393e07c0c36a4ab5b6f217d695440cbea0e2'],
+    }),
+    ('pathview', '1.38.0', {
+        'checksums': ['fe12df8ffa7cb6cb0d76d2aa32029f41df37a00f3adf0400bf7f1834006eec5c'],
+    }),
+    ('chromVAR', '1.20.2', {
+        'checksums': ['5f84ba3ea747f136a682c8c67c7119e2182f26abfe0b658344aa374d03b2910c'],
+    }),
+    ('EnsDb.Hsapiens.v79', '2.99.0', {
+        'checksums': ['eff1ae8d7f4ed5c6bed335de63a758be593750fb0b3483c01cf50402688d244d'],
+    }),
+    ('WGCNA', '1.72-1', {
+        'checksums': ['1dbf82761ef3e76464b18fc9f698ad0f971aafecabf66ca937b950930bd57fdc'],
+    }),
+    ('DNABarcodes', '1.28.0', {
+        'checksums': ['2596c0eb02789418b4522cbbc5a99c191d5e238940530e6d13653e443fdf51a3'],
+    }),
+    ('CAGEr', '2.4.0', {
+        'checksums': ['e026e29d8f86bf2ba934bb6bf22b290ea833365dd499ebc996d65e31a2928ad1'],
+    }),
+    ('SPOTlight', '1.2.0', {
+        'checksums': ['6e3b6e011952cf37c10efaa1ef248c37c8735d492225f5e7b7fc9319325cfb0f'],
+    }),
+    ('CGHcall', '2.60.0', {
+        'checksums': ['e289c5e932e86db0f98233c6de2893860cea0bea4dde0462c45818e3b6e0c020'],
+    }),
+    ('QDNAseq', '1.34.0', {
+        'checksums': ['a968daf40745cc54b48bfe6c2a105d631f88deaeb09008f12d239f6858dd63e3'],
+    }),
+    ('HiCcompare', '1.20.0', {
+        'checksums': ['ae4adc96ef85b0675d2089207ad756dd14152e9127db66cf5b034c07ee1a7b43'],
+    }),
+    ('ROntoTools', '2.26.0', {
+        'checksums': ['1a60b08689b2878761188298cf1969e096741f560e96608612b6ed9145671174'],
+    }),
+    ('scDblFinder', '1.12.0', {
+        'checksums': ['f1eb33ad022e4d1c007f9dae72efb05a3c183cd6eb576794b9a0339f9180543f'],
+    }),
+    ('treeio', '1.22.0', {
+        'checksums': ['892283d09694dd4cc7111118647612d1f2fcd2b730bab1c7a5301de54f2288f6'],
+    }),
+    ('ggtree', '3.6.2', {
+        'checksums': ['bdca865db5cfc5b4aa89f62e185b31d3f1de87658609a7bfe9e0769895c1f69c'],
+    }),
+    ('scistreer', '1.1.0', {
+        'checksums': ['49936bcbb107423d96aee421334c4ac6a1048434d2621b84eab95cf7ac11b731'],
+    }),
+    ('numbat', '1.2.2', {
+        'checksums': ['0c567b26f7ff9a6c2129f9c023ffe6eaccea441b73b91cc3f327d630513c181b'],
+    }),
+    ('HiCBricks', '1.16.0', {
+        'checksums': ['d41a7600003b62ff04e3e3ddbc62e494c325207b3da720e5acefcc03ad06a80e'],
+    }),
+    ('dir.expiry', '1.6.0', {
+        'checksums': ['c8157d9ea86ad244923b344fe39bd73931fe2399e46ba0ae08af8de8980ca3c7'],
+    }),
+    ('basilisk.utils', '1.10.0', {
+        'checksums': ['dca17bf5ca9ae225258241744a9829c71fb07b5450f37cb9a20fbcac104f023e'],
+    }),
+    ('basilisk', '1.10.2', {
+        'checksums': ['09b402dae2d9328f76d7ffb91311cde639e55c967462ed279345caa3e2a84f93'],
+    }),
+    ('zellkonverter', '1.8.0', {
+        'checksums': ['bed7c72324df7882816e594ccd8d6b84f5575999491c89a4ab5739e8a9d9242c'],
+    }),
+    ('DO.db', '2.9', {
+        'checksums': ['762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881'],
+    }),
+    ('GOSemSim', '2.24.0', {
+        'checksums': ['5a78ea253c1c34ef0b2c479eaef295eb766c81658688021ab553df301f3e8c93'],
+    }),
+    ('HDO.db', '0.99.1', {
+        'checksums': ['c17cf28d06621d91148a64d47fdeaa906d8621aba7a688715fb9571a55f7cf92'],
+    }),
+    ('DOSE', '3.24.2', {
+        'checksums': ['6fec12b1d5f622f5606236d559c801072d185c6f64aaf60e749cc7b09e369769'],
+    }),
+    ('enrichplot', '1.18.3', {
+        'checksums': ['f483d3a8e7210a772acec74b4728a3f14812be11ae67072c80e3a35287c8ec5b'],
+    }),
+    ('gson', '0.1.0', {
+        'checksums': ['14ddbee5be66d0b1dc178e41175a50ab6ed9ffed04d4361ecf5eef3548d9a381'],
+    }),
+    ('clusterProfiler', '4.6.2', {
+        'checksums': ['af014c40f46646db0a5b6ef883af6e04010b5c1c0c33b8ff5d30336e43c3fc04'],
+    }),
+    ('reactome.db', '1.82.0', {
+        'checksums': ['82f013e2bf42580c039af74a7fddba17e445cdb4845f95ccd61cfd07bc3cd350'],
+    }),
+    ('graphite', '1.44.0', {
+        'checksums': ['1ccca351d2f6e6c90e76b6a899b08b83a95241a67c1546f50e4f312bc252723e'],
+    }),
+    ('ReactomePA', '1.42.0', {
+        'checksums': ['c2c55cf86b81841303952d9c4d4acac1ad964d31c1f8a5d17ff4679b26242919'],
+    }),
+    ('flowClean', '1.36.0', {
+        'checksums': ['732848b879f4d7bb5b9b4cbef32a6980e93b28fd92913b08456736c01dc21cf3'],
+    }),
+    ('flowAI', '1.28.0', {
+        'checksums': ['e9995350f3076a42f8e9fc65c8cafded12924947da17c361a72f26c4a5a5f9a3'],
+    }),
+    ('flowFP', '1.56.3', {
+        'checksums': ['fe64504cdb419adbb4342686ef0c99906c0071cc626ac12bba9d3161ed3ec611'],
+    }),
+    ('simplifyEnrichment', '1.8.0', {
+        'checksums': ['fe492daf93f39c34b47340182e008ac7140eeb14d02a4e9961f47d693c2c1d8c'],
+    }),
+    ('RPMG', '2.2-3', {
+        'checksums': ['74d5bada6a51d280296cb36fae4938c16ba9ed2fa37f3bfb60cf7c541c5b22b6'],
+    }),
+    ('Rwave', '2.6-5', {
+        'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'],
+    }),
+    ('RSEIS', '4.1-4', {
+        'checksums': ['76d5caf30cd3871fa80d27ea694023a4c303ffc099297aeeff03d22538dbff76'],
+    }),
+    ('splancs', '2.01-43', {
+        'checksums': ['b351565e1f69f6c86a29d921d3a18d5896c4586e2ab8c73bb3df8e75630fc448'],
+    }),
+    ('MBA', '0.1-0', {
+        'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'],
+    }),
+    ('GEOmap', '2.5-0', {
+        'checksums': ['82e5608eda7330632bc67aa662b649e7b7b3ccdfda6a18a19d2e3379e0db1093'],
+    }),
+    ('RFOC', '3.4-6', {
+        'checksums': ['0dfa237f4d04eb9a2718942b4d7ed9538fc5f89e3cbaa5a34a4fd1bc6fe54533'],
+    }),
+    ('flowDensity', '1.32.0', {
+        'checksums': ['4977c5a2723a034a9fb9458bfba00f917fa87182af35198f82d24d75f4c1d4bd'],
+    }),
+    ('flowPeaks', '1.44.0', {
+        'checksums': ['97ad0e513cfb954eef35445ee085d1d6268d0ab2a8ec4e73d6456ea6d25a7a58'],
+    }),
+    ('SamSPECTRAL', '1.52.0', {
+        'checksums': ['b8f85ce42b62b42c6fe6fd7fac7501e4329a359ad9126190207da9607c88f0ea'],
+    }),
+    ('ddPCRclust', '1.18.0', {
+        'checksums': ['c27706a922d11d49a0a4f269df9de6882d81140eecf8a726220cd52b6db8372c'],
+    }),
+    ('feature', '1.2.15', {
+        'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'],
+    }),
+    ('flowMerge', '2.46.0', {
+        'checksums': ['3634723fd87b1bae71e2cd9e646e98cecc891521b4f2e9ff3ff388362b8b21eb'],
+    }),
+    ('SpatialExperiment', '1.8.1', {
+        'checksums': ['0fdfc5642dde227b73d81812b6641f2d10223de66892b9d61ac80664cd6cbacd'],
+    }),
+]
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'],
+}
+
+moduleclass = 'bio'

From 3789ac9c63f7c98a77eaa4b8a0de7a70a954924c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 11:14:21 +0100
Subject: [PATCH 109/601] remove unused variable, add comment to patch

---
 .../torchtext/torchtext-0.14.1-foss-2022a.eb  | 45 +++++++++++++++++++
 .../torchtext/torchtext-0.14.1_deps_fix.patch |  1 +
 2 files changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
new file mode 100644
index 00000000000..cb3a29fdcce
--- /dev/null
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
@@ -0,0 +1,45 @@
+easyblock = 'PythonPackage'
+
+name = 'torchtext'
+version = '0.14.1'
+local_pytorch_version = '1.12.0'
+local_python_suffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/pytorch/text'
+description = "Data loaders and abstractions for text and NLP"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# Sources are no longer available in PyPI, it only has wheels
+source_urls = ['https://github.com/pytorch/text/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['torchtext-0.14.1_deps_fix.patch']
+checksums = [
+    {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
+    {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'},
+]
+
+builddependencies = [
+    ('RE2', '2022-06-01'),
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('SentencePiece', '0.1.97'),
+    ('tqdm', '4.64.0'),
+    ('PyTorch', local_pytorch_version),
+    ('double-conversion', '3.2.0'),
+    ('utf8proc', '2.7.0'),
+]
+
+download_dep_fail = True,
+use_pip = True
+sanity_pip_check = True,
+
+# Disable bundled libraries to use those from EB: RE2, SentencePiece
+preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && "
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch
index ab7a71f24f5..1212651426e 100644
--- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch
@@ -1,3 +1,4 @@
+The error "string_view has not been declared in std" appears when not using C++17
 diff -u text/CMakeLists.txt.orig text/CMakeLists.txt
 --- text/CMakeLists.txt.orig	2023-03-08 14:33:35.618931003 +0100
 +++ text/CMakeLists.txt	2023-03-08 14:35:03.169072623 +0100

From c89af4e593b2ae6a3bf151e030fb410c0f68fedd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 20 Mar 2023 11:21:11 +0100
Subject: [PATCH 110/601] adding easyconfigs: EasyBuild-4.7.1.eb

---
 .../e/EasyBuild/EasyBuild-4.7.1.eb            | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb

diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb
new file mode 100644
index 00000000000..8d9ac53bb93
--- /dev/null
+++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb
@@ -0,0 +1,45 @@
+easyblock = 'EB_EasyBuildMeta'
+
+name = 'EasyBuild'
+version = '4.7.1'
+
+homepage = 'https://easybuilders.github.io/easybuild'
+description = """EasyBuild is a software build and installation framework
+ written in Python that allows you to install software in a structured,
+ repeatable and robust way."""
+
+toolchain = SYSTEM
+
+source_urls = [
+    # easybuild-framework
+    'https://files.pythonhosted.org/packages/76/4b/b7a88e791cce0d79db9f2319ab07c79584815ca9e497d178c39fa4621b8d/',
+    # easybuild-easyblocks
+    'https://files.pythonhosted.org/packages/10/72/391eb5bde081da67fef0a59625ce7cf4939176416aed299ef55923e422b4/',
+    # easybuild-easyconfigs
+    'https://files.pythonhosted.org/packages/32/1a/e7c851db23ffb0fc5c3cc9c255318d533f642c86eff2c3c33e0ab063a449/',
+
+]
+sources = [
+    'easybuild-framework-%(version)s.tar.gz',
+    'easybuild-easyblocks-%(version)s.tar.gz',
+    'easybuild-easyconfigs-%(version)s.tar.gz',
+]
+checksums = [
+    {'easybuild-framework-4.7.1.tar.gz': 'ad3d95c2b11f895666d83cda3422e785261ecb9d14e7c3e0c9cef427b7404d6b'},
+    {'easybuild-easyblocks-4.7.1.tar.gz': '8c383dc4d02784e5ab610cec2df58c19ff9c1b7c03bb7585788ced1646e394e8'},
+    {'easybuild-easyconfigs-4.7.1.tar.gz': '58c70e7e4a8958f932e4e7abab0194198a8f9baf19915bfa5191b431f3f1a864'},
+]
+
+# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?)
+# EasyBuild is a (set of) Python packages, so it depends on Python
+# usually, we want to use the system Python, so no actual Python dependency is listed
+allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2])
+
+sanity_check_paths = {
+    'files': ['bin/eb'],
+    'dirs': ['lib/python%s/site-packages' % local_pyshortver],
+}
+
+moduleclass = 'tools'

From c88271d0069b4b3f7e8af9747218285e43bfe00b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 11:34:46 +0100
Subject: [PATCH 111/601] bring back the suffix variable, delete unwanted file

---
 .../torchtext/torchtext-0.14.1-foss-2022a.eb  | 45 -------------------
 1 file changed, 45 deletions(-)
 delete mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
deleted file mode 100644
index cb3a29fdcce..00000000000
--- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
+++ /dev/null
@@ -1,45 +0,0 @@
-easyblock = 'PythonPackage'
-
-name = 'torchtext'
-version = '0.14.1'
-local_pytorch_version = '1.12.0'
-local_python_suffix = '-Python-%(pyver)s'
-
-homepage = 'https://github.com/pytorch/text'
-description = "Data loaders and abstractions for text and NLP"
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-# Sources are no longer available in PyPI, it only has wheels
-source_urls = ['https://github.com/pytorch/text/archive/']
-sources = ['v%(version)s.tar.gz']
-patches = ['torchtext-0.14.1_deps_fix.patch']
-checksums = [
-    {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
-    {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'},
-]
-
-builddependencies = [
-    ('RE2', '2022-06-01'),
-    ('binutils', '2.38'),
-    ('CMake', '3.24.3'),
-]
-
-dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('SentencePiece', '0.1.97'),
-    ('tqdm', '4.64.0'),
-    ('PyTorch', local_pytorch_version),
-    ('double-conversion', '3.2.0'),
-    ('utf8proc', '2.7.0'),
-]
-
-download_dep_fail = True,
-use_pip = True
-sanity_pip_check = True,
-
-# Disable bundled libraries to use those from EB: RE2, SentencePiece
-preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && "
-
-moduleclass = 'tools'

From a4cf2650135fa343eb4d76a66ac163da506ab76d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 11:40:48 +0100
Subject: [PATCH 112/601] fix checksum of patch file

---
 .../torchtext/torchtext-0.14.1-foss-2022a.eb  | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
new file mode 100644
index 00000000000..cb3a29fdcce
--- /dev/null
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
@@ -0,0 +1,45 @@
+easyblock = 'PythonPackage'
+
+name = 'torchtext'
+version = '0.14.1'
+local_pytorch_version = '1.12.0'
+local_python_suffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/pytorch/text'
+description = "Data loaders and abstractions for text and NLP"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# Sources are no longer available in PyPI, it only has wheels
+source_urls = ['https://github.com/pytorch/text/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['torchtext-0.14.1_deps_fix.patch']
+checksums = [
+    {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
+    {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'},
+]
+
+builddependencies = [
+    ('RE2', '2022-06-01'),
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('SentencePiece', '0.1.97'),
+    ('tqdm', '4.64.0'),
+    ('PyTorch', local_pytorch_version),
+    ('double-conversion', '3.2.0'),
+    ('utf8proc', '2.7.0'),
+]
+
+download_dep_fail = True,
+use_pip = True
+sanity_pip_check = True,
+
+# Disable bundled libraries to use those from EB: RE2, SentencePiece
+preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && "
+
+moduleclass = 'tools'

From 287f6d52213fd1a904f5d767e01f2e7e49466e81 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 12:10:29 +0100
Subject: [PATCH 113/601] Delete torchtext-0.14.1-foss-2022a.eb

---
 .../torchtext/torchtext-0.14.1-foss-2022a.eb  | 45 -------------------
 1 file changed, 45 deletions(-)
 delete mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
deleted file mode 100644
index cb3a29fdcce..00000000000
--- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
+++ /dev/null
@@ -1,45 +0,0 @@
-easyblock = 'PythonPackage'
-
-name = 'torchtext'
-version = '0.14.1'
-local_pytorch_version = '1.12.0'
-local_python_suffix = '-Python-%(pyver)s'
-
-homepage = 'https://github.com/pytorch/text'
-description = "Data loaders and abstractions for text and NLP"
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-# Sources are no longer available in PyPI, it only has wheels
-source_urls = ['https://github.com/pytorch/text/archive/']
-sources = ['v%(version)s.tar.gz']
-patches = ['torchtext-0.14.1_deps_fix.patch']
-checksums = [
-    {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
-    {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'},
-]
-
-builddependencies = [
-    ('RE2', '2022-06-01'),
-    ('binutils', '2.38'),
-    ('CMake', '3.24.3'),
-]
-
-dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('SentencePiece', '0.1.97'),
-    ('tqdm', '4.64.0'),
-    ('PyTorch', local_pytorch_version),
-    ('double-conversion', '3.2.0'),
-    ('utf8proc', '2.7.0'),
-]
-
-download_dep_fail = True,
-use_pip = True
-sanity_pip_check = True,
-
-# Disable bundled libraries to use those from EB: RE2, SentencePiece
-preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && "
-
-moduleclass = 'tools'

From b6960c3919fe4483b20d9d5f054f6f68c71494c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 12:11:38 +0100
Subject: [PATCH 114/601] fix checksum of patch file

---
 .../torchtext/torchtext-0.14.1-foss-2022a.eb  | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
new file mode 100644
index 00000000000..cb3a29fdcce
--- /dev/null
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
@@ -0,0 +1,45 @@
+easyblock = 'PythonPackage'
+
+name = 'torchtext'
+version = '0.14.1'
+local_pytorch_version = '1.12.0'
+local_python_suffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/pytorch/text'
+description = "Data loaders and abstractions for text and NLP"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# Sources are no longer available in PyPI, it only has wheels
+source_urls = ['https://github.com/pytorch/text/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['torchtext-0.14.1_deps_fix.patch']
+checksums = [
+    {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
+    {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'},
+]
+
+builddependencies = [
+    ('RE2', '2022-06-01'),
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('SentencePiece', '0.1.97'),
+    ('tqdm', '4.64.0'),
+    ('PyTorch', local_pytorch_version),
+    ('double-conversion', '3.2.0'),
+    ('utf8proc', '2.7.0'),
+]
+
+download_dep_fail = True,
+use_pip = True
+sanity_pip_check = True,
+
+# Disable bundled libraries to use those from EB: RE2, SentencePiece
+preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && "
+
+moduleclass = 'tools'

From d911fa61b036bfaacd9245678c6b7e137470fa9c Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Mon, 20 Mar 2023 13:22:14 +0100
Subject: [PATCH 115/601] adding easyconfigs: KrakenUniq-1.0.3-foss-2022a.eb

---
 .../KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb

diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
new file mode 100644
index 00000000000..e50cc310ceb
--- /dev/null
+++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
@@ -0,0 +1,33 @@
+easyblock = 'Binary'
+
+name = 'KrakenUniq'
+version = '1.0.3'
+
+homepage = 'https://github.com/fbreitwieser/krakenuniq/'
+description = """KrakenUniq: confident and fast metagenomics classification using unique k-mer counts"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+github_account = 'fbreitwieser'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['559b45081688118b4872e1b9153f83d0ae3414649a1b299ab4f9996d9e154403']
+
+dependencies = [
+    ('Jellyfish', '2.3.0'),
+]
+
+extract_sources = True
+
+install_cmd = './install_krakenuniq.sh -l %(installdir)s/bin %(installdir)s '
+
+sanity_check_commands = [
+    'krakenuniq --version',
+    'krakenuniq-download --db %(installdir)s/DBDIR taxonomy && rm -r %(installdir)s/DBDIR'
+]
+sanity_check_paths = {
+    'files': ['bin/krakenuniq', 'bin/krakenuniq-build', 'bin/krakenuniq-report'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'bio'

From 61630473c5dc738ae38eb326497144307f44a60e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 13:30:03 +0100
Subject: [PATCH 116/601] update patchfile checksum, delete unwanted file

---
 ...chtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb |  3 +-
 .../torchtext/torchtext-0.14.1-foss-2022a.eb  | 45 -------------------
 2 files changed, 1 insertion(+), 47 deletions(-)
 delete mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
index 46bf098eddc..cb3a29fdcce 100644
--- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
@@ -4,7 +4,6 @@ name = 'torchtext'
 version = '0.14.1'
 local_pytorch_version = '1.12.0'
 local_python_suffix = '-Python-%(pyver)s'
-versionsuffix = '-PyTorch-%s' % local_pytorch_version
 
 homepage = 'https://github.com/pytorch/text'
 description = "Data loaders and abstractions for text and NLP"
@@ -17,7 +16,7 @@ sources = ['v%(version)s.tar.gz']
 patches = ['torchtext-0.14.1_deps_fix.patch']
 checksums = [
     {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
-    {'torchtext-0.14.1_deps_fix.patch': '38ee9a2c74016376ef3ff06ea40eb4522f5a72410573168050b79cab457077c7'},
+    {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'},
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
deleted file mode 100644
index cb3a29fdcce..00000000000
--- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb
+++ /dev/null
@@ -1,45 +0,0 @@
-easyblock = 'PythonPackage'
-
-name = 'torchtext'
-version = '0.14.1'
-local_pytorch_version = '1.12.0'
-local_python_suffix = '-Python-%(pyver)s'
-
-homepage = 'https://github.com/pytorch/text'
-description = "Data loaders and abstractions for text and NLP"
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-# Sources are no longer available in PyPI, it only has wheels
-source_urls = ['https://github.com/pytorch/text/archive/']
-sources = ['v%(version)s.tar.gz']
-patches = ['torchtext-0.14.1_deps_fix.patch']
-checksums = [
-    {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'},
-    {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'},
-]
-
-builddependencies = [
-    ('RE2', '2022-06-01'),
-    ('binutils', '2.38'),
-    ('CMake', '3.24.3'),
-]
-
-dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('SentencePiece', '0.1.97'),
-    ('tqdm', '4.64.0'),
-    ('PyTorch', local_pytorch_version),
-    ('double-conversion', '3.2.0'),
-    ('utf8proc', '2.7.0'),
-]
-
-download_dep_fail = True,
-use_pip = True
-sanity_pip_check = True,
-
-# Disable bundled libraries to use those from EB: RE2, SentencePiece
-preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && "
-
-moduleclass = 'tools'

From 15f88ab2555a5e134a8a8e07cc45bdfd71dce702 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 13:54:42 +0100
Subject: [PATCH 117/601] adding easyconfigs: SHAP-0.41.0-foss-2022a.eb

---
 .../s/SHAP/SHAP-0.41.0-foss-2022a.eb          | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb
new file mode 100644
index 00000000000..0e5be094112
--- /dev/null
+++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'SHAP'
+version = '0.41.0'
+
+homepage = "https://github.com/slundberg/shap"
+description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any
+ machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley
+ values from game theory and their related extensions."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('scikit-learn', '1.1.2'),
+    ('tqdm', '4.64.0'),
+    ('numba', '0.56.4'),
+]
+
+# Python 3.10.4 uses poetry 1.1.13 which needs packaging "^20.4"
+preinstallopts = "sed -i 's/packaging>20.9/packaging/g' setup.py && "
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('cloudpickle', '2.2.1', {
+        'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'],
+    }),
+    ('slicer', '0.0.7', {
+        'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'],
+    }),
+    (name, version, {
+        'modulename': '%(namelower)s',
+        'sources': [SOURCELOWER_TAR_GZ],
+        'checksums': ['a49ea4d65aadbc845a695fa3d7ea0bdfc8c928b8e213b0feedf5868ade4b3ca5'],
+    }),
+]
+
+moduleclass = 'data'

From d591ffcdab9d5b7471607cf354fe4ece42618934 Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Mon, 20 Mar 2023 14:00:19 +0100
Subject: [PATCH 118/601] solving missing bzlib

---
 .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
index e50cc310ceb..d742f03d6fb 100644
--- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
@@ -15,6 +15,7 @@ checksums = ['559b45081688118b4872e1b9153f83d0ae3414649a1b299ab4f9996d9e154403']
 
 dependencies = [
     ('Jellyfish', '2.3.0'),
+    ('bzip2', '1.0.8'),
 ]
 
 extract_sources = True

From e9d94c1a3c9fc26f5c2c2f0e4e545528ad4d6841 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 14:00:31 +0100
Subject: [PATCH 119/601] adding easyconfigs: pydantic-1.10.4-GCCcore-11.3.0.eb

---
 .../pydantic-1.10.4-GCCcore-11.3.0.eb         | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..796120e325e
--- /dev/null
+++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonBundle'
+
+name = 'pydantic'
+version = '1.10.4'
+
+homepage = 'https://github.com/samuelcolvin/pydantic'
+description = """Data validation and settings management using Python type hinting."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('typing_extensions', '4.4.0', {
+        'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'],
+    }),
+    (name, version, {
+        'checksums': ['b9a3859f24eb4e097502a3be1fb4b2abb79b6103dd9e2e0edb70613a4459a648'],
+    }),
+]
+
+moduleclass = 'devel'

From 1051fc99e768fc24ce777f5d9cdc21fdbab1cab0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 14:05:56 +0100
Subject: [PATCH 120/601] adding easyconfigs: lifelines-0.27.4-foss-2022a.eb

---
 .../lifelines/lifelines-0.27.4-foss-2022a.eb  | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb
new file mode 100644
index 00000000000..c300ce4d3a6
--- /dev/null
+++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb
@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'lifelines'
+version = '0.27.4'
+
+homepage = "https://lifelines.readthedocs.io/en/latest/"
+description = """lifelines is a complete survival analysis library, written in pure Python."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('wrapt', '1.14.1', {
+        'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'],
+    }),
+    ('astor', '0.8.1', {
+        'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
+    }),
+    ('interface_meta', '1.3.0', {
+        'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'],
+    }),
+    ('autograd', '1.5', {
+        'checksums': ['d80bd225154d1db13cb4eaccf7a18c358be72092641b68717f96fcf1d16acd0b'],
+    }),
+    ('autograd-gamma', '0.5.0', {
+        'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'],
+    }),
+    ('formulaic', '0.4.0', {
+        'checksums': ['087950518c53a2491deb52b8ddd66833f953882e517a42e476c007cc8f6892c5'],
+    }),
+    (name, version, {
+        'checksums': ['62f7e911a64c8f723eef4207174fb1df39a94f79eca557cdf53d310eb6be132f'],
+    }),
+]
+
+moduleclass = 'bio'

From 4b8bceb54c4bbeddff43de4fe139a4910aedb914 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 14:07:40 +0100
Subject: [PATCH 121/601] fix suffix

---
 .../t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
index cb3a29fdcce..4a649652439 100644
--- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
+++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb
@@ -3,7 +3,7 @@ easyblock = 'PythonPackage'
 name = 'torchtext'
 version = '0.14.1'
 local_pytorch_version = '1.12.0'
-local_python_suffix = '-Python-%(pyver)s'
+versionsuffix = '-PyTorch-%s' % local_pytorch_version
 
 homepage = 'https://github.com/pytorch/text'
 description = "Data loaders and abstractions for text and NLP"

From 1e4836a88a83c79de874ca6e5b4a1b0b16b546ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 20 Mar 2023 14:57:48 +0100
Subject: [PATCH 122/601] adding easyconfigs: CPLEX-22.1.1-GCCcore-11.2.0.eb

---
 .../c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb    | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb
new file mode 100644
index 00000000000..d788295e132
--- /dev/null
+++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb
@@ -0,0 +1,26 @@
+name = 'CPLEX'
+version = '22.1.1'
+
+homepage = 'https://www.ibm.com/analytics/cplex-optimizer'
+description = """IBM ILOG CPLEX Optimizer's mathematical programming technology enables
+ analytical decision support for improving efficiency,
+ reducing costs, and increasing profitability."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+sources = ['cplex_studio%s.linux_x86_64.bin' % ''.join(version.split('.'))]
+checksums = ['ab6d3f0953fdb3cbd43854452357955ef96db8b751c0866de3572fc47a0df542']
+
+download_instructions = """
+1. Visit https://www.ibm.com/products/ilog-cplex-optimization-studio
+2. Sign up and download the Academic Edition
+"""
+
+builddependencies = [('binutils', '2.37')]
+
+dependencies = [
+    ('Java', '11', '', SYSTEM),
+    ('Python', '3.9.6'),
+]
+
+moduleclass = 'math'

From 5ab249e95af3a538d979a30d8483397322930bda Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Mon, 20 Mar 2023 15:16:51 +0100
Subject: [PATCH 123/601] adding easyconfigs:
 pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb

---
 ...sing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb

diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb
new file mode 100644
index 00000000000..9ef3f6d433b
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb
@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'pyparsing'
+version = '3.0.9'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/pyparsing/pyparsing'
+description = """The pyparsing module is an alternative approach to creating and
+executing simple grammars, vs. the traditional lex/yacc approach, or the use of
+regular expressions. The pyparsing module provides a library of classes that
+client code uses to construct the grammar directly in Python code."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb']
+
+moduleclass = 'data'

From e4d3dcbce9ed323b2f706b86d3fffe87d4122643 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Mon, 20 Mar 2023 18:55:03 +0100
Subject: [PATCH 124/601] adding easyconfigs: spdlog-1.11.0-GCCcore-12.2.0.eb

---
 .../s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb  | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..37e99e71124
--- /dev/null
+++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'CMakeMake'
+
+name = 'spdlog'
+version = '1.11.0'
+
+homepage = 'https://github.com/gabime/spdlog'
+description = 'Very fast, header-only/compiled, C++ logging library.'
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['ca5cae8d6cac15dae0ec63b21d6ad3530070650f68076f3a4a862ca293a858bb']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/spdlog/spdlog.h'],
+    'dirs': ['lib64/cmake', 'lib64/pkgconfig'],
+}
+
+moduleclass = 'lib'

From 33d910cd108dd76c3999da0d7adced27e8b7aae4 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Mon, 20 Mar 2023 18:55:46 +0100
Subject: [PATCH 125/601] adding easyconfigs: fmt-9.1.0-GCCcore-12.2.0.eb

---
 .../f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb         | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..cfaa82feaea
--- /dev/null
+++ b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'fmt'
+version = '9.1.0'
+
+homepage = 'http://fmtlib.net/'
+description = "fmt (formerly cppformat) is an open-source formatting library."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/']
+sources = ['fmt-%(version)s.zip']
+checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('binutils', '2.39')
+]
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['lib/libfmt.a'],
+    'dirs': ['include/fmt', 'lib/cmake'],
+}
+
+moduleclass = 'lib'

From 225d47e7c6783cc531fa3f14c9b21d1ff728aca0 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Mon, 20 Mar 2023 17:57:18 +0000
Subject: [PATCH 126/601] Sanity check path removed

---
 easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
index 0526cbdc186..dbe91a2e7ff 100644
--- a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
+++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb
@@ -39,9 +39,4 @@ exts_list = [
     }),
 ]
 
-sanity_check_paths = {
-    'files': [],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
-}
-
 moduleclass = 'tools'

From 171372902ed35fdadd81e23907a7b15b7aa50e01 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 20 Mar 2023 16:34:26 +0100
Subject: [PATCH 127/601] bump version to 4.7.2dev

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 3820ff609f1..1e5caaddac1 100644
--- a/setup.py
+++ b/setup.py
@@ -44,7 +44,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = '4.7.1'
+VERSION = '4.7.2.dev0'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])

From e2f97d72860a699ddd91d4598b06d41297dc08f9 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Mon, 20 Mar 2023 19:07:21 +0100
Subject: [PATCH 128/601] adding easyconfigs:
 CapnProto-0.10.3-GCCcore-12.2.0.eb

---
 .../CapnProto-0.10.3-GCCcore-12.2.0.eb        | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..ee6242554c7
--- /dev/null
+++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb
@@ -0,0 +1,35 @@
+# Contribution by
+# DeepThought, Flinders University
+# Updated to 0.9.1
+# R.QIAO <rob.qiao@flinders.edu.au>
+
+easyblock = 'ConfigureMake'
+
+name = 'CapnProto'
+version = '0.10.3'
+
+homepage = 'https://capnproto.org'
+description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope"
+# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..."
+# (only on Intel Skylake?)
+toolchainopts = {'cstd': 'c++17', 'lowopt': True}
+
+source_urls = ['https://capnproto.org/']
+sources = ['capnproto-c++-%(version)s.tar.gz']
+checksums = ['97fde3cf05129db919453af4ef6c6a415662111c2e6e9b5194e2566d44b8507a']
+
+builddependencies = [('binutils', '2.39')]
+
+local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': ['include/capnp', 'include/kj', 'lib'],
+}
+
+sanity_check_commands = ["%s --help" % x for x in local_bins]
+
+moduleclass = 'bio'

From ddf4e345925818eb40b0e150cd8a1d3c4743347b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 21 Mar 2023 02:49:58 +0100
Subject: [PATCH 129/601] Delete avro-cpp-1.11.1-GCCcore-11.2.0.eb

---
 .../avro-cpp-1.11.1-GCCcore-11.2.0.eb         | 36 -------------------
 1 file changed, 36 deletions(-)
 delete mode 100644 easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb
deleted file mode 100644
index 17e21b86b52..00000000000
--- a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb
+++ /dev/null
@@ -1,36 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'avro-cpp'
-version = '1.11.1'
-
-homepage = 'https://avro.apache.org'
-description = """C++ implementation of Avro data serialization system."""
-
-toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
-
-source_urls = ['https://github.com/apache/avro/archive/refs/tags/']
-sources = ['release-%(version)s.tar.gz']
-checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752']
-
-builddependencies = [
-    ('binutils', '2.37'),
-    ('CMake', '3.22.1'),
-]
-
-dependencies = [
-    ('Boost', '1.77.0', '', ('GCC', '11.2.0')),
-]
-
-srcdir = "lang/c++"
-
-generator = "Unix Makefiles"
-separate_build_dir = True
-
-sanity_check_paths = {
-    'files': ["bin/avrogencpp"],
-    'dirs': ["lib"],
-}
-
-sanity_check_commands = ["avrogencpp -h"]
-
-moduleclass = 'lib'

From ef8a6939520cd874267e76b51fbe20c75993b30a Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Tue, 21 Mar 2023 08:53:12 +0100
Subject: [PATCH 130/601] Moving ASE from foss to gfbf

---
 .../ASE/{ASE-3.22.1-foss-2022b.eb => ASE-3.22.1-gfbf-2022b.eb}  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename easybuild/easyconfigs/a/ASE/{ASE-3.22.1-foss-2022b.eb => ASE-3.22.1-gfbf-2022b.eb} (97%)

diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb
similarity index 97%
rename from easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb
rename to easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb
index 4a076fc342b..d2486e7b79e 100644
--- a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb
@@ -10,7 +10,7 @@ description = """ASE is a python package providing an open source Atomic Simulat
 From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations
 in C of functions in ASE.  ASE uses it automatically when installed."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'gfbf', 'version': '2022b'}
 
 dependencies = [
     ('Python', '3.10.8'),

From a1034c1d493638a8992e4ca14cbe3fcf51f0c7a4 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Tue, 21 Mar 2023 14:46:32 +0000
Subject: [PATCH 131/601] Update KrakenUniq-1.0.3-foss-2022a.eb

review changes
---
 .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
index d742f03d6fb..5d22642632a 100644
--- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
@@ -6,7 +6,7 @@ version = '1.0.3'
 homepage = 'https://github.com/fbreitwieser/krakenuniq/'
 description = """KrakenUniq: confident and fast metagenomics classification using unique k-mer counts"""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'GCCCore', 'version': '11.3.0'}
 
 github_account = 'fbreitwieser'
 source_urls = [GITHUB_SOURCE]
@@ -15,6 +15,7 @@ checksums = ['559b45081688118b4872e1b9153f83d0ae3414649a1b299ab4f9996d9e154403']
 
 dependencies = [
     ('Jellyfish', '2.3.0'),
+    ('Perl', '5.34.1'),
     ('bzip2', '1.0.8'),
 ]
 

From a17648a58355accc6ddfdf40629b3aa4965932d0 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Tue, 21 Mar 2023 14:50:10 +0000
Subject: [PATCH 132/601] Update KrakenUniq-1.0.3-foss-2022a.eb

typo
---
 .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
index 5d22642632a..1f52ef21a7d 100644
--- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
@@ -6,7 +6,7 @@ version = '1.0.3'
 homepage = 'https://github.com/fbreitwieser/krakenuniq/'
 description = """KrakenUniq: confident and fast metagenomics classification using unique k-mer counts"""
 
-toolchain = {'name': 'GCCCore', 'version': '11.3.0'}
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
 
 github_account = 'fbreitwieser'
 source_urls = [GITHUB_SOURCE]

From f6cfee5eac1db2ad8c0030e64e0bae09f99e167b Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 21 Mar 2023 16:54:40 +0100
Subject: [PATCH 133/601] adding easyconfigs:
 ruamel.yaml-0.17.21-GCCcore-12.2.0.eb

---
 .../ruamel.yaml-0.17.21-GCCcore-12.2.0.eb     | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..e74ae172df4
--- /dev/null
+++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb
@@ -0,0 +1,55 @@
+easyblock = 'PythonBundle'
+
+name = 'ruamel.yaml'
+version = '0.17.21'
+
+homepage = 'https://sourceforge.net/projects/ruamel-yaml'
+description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('ruamel.yaml.clib', '0.2.7', {
+        'modulename': False,
+        'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'],
+    }),
+    (name, version, {
+        'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'],
+    }),
+    ('configobj', '5.0.8', {
+        'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'],
+    }),
+    ('lz4', '4.3.2', {
+        'checksums': ['e1431d84a9cfb23e6773e72078ce8e65cad6745816d4cbf9ae67da5ea419acda'],
+    }),
+    ('ruamel.yaml.base', '0.3.2', {
+        'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'],
+    }),
+    ('ruamel.yaml.convert', '0.3.2', {
+        'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'],
+    }),
+    ('ruamel.yaml.cmd', '0.6.3', {
+        'checksums': ['f4ebce7d6d9d53afae84d7efd79f8d6c3dcad56e0e6be3a5d2370be0e04acea0'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/yaml'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["yaml --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

From 89b7512fdc07f6dc64d9211a41900d5bf773b326 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Mar 2023 17:12:19 +0100
Subject: [PATCH 134/601] remove preinstallopts to break import of Crypto, no
 longer needed since pycrypto was replaced with pycryptodome in #17412

---
 .../easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb    | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb
index 98f87e55a48..e9af6f66373 100644
--- a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb
+++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb
@@ -27,13 +27,9 @@ exts_list = [
     }),
     ('pypdf', '3.4.1', {
         'checksums': ['8b0badc787062e8fb0d8393eb2a76903717fb24e5cc84e2b03cde5ac3881700f'],
-        # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x
-        'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' pypdf/_encryption.py && ",
     }),
     ('PyPDF2', '3.0.1', {
         'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'],
-        # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x
-        'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' PyPDF2/_encryption.py && ",
         'modulename': 'PyPDF2',
     }),
     ('PyPDF3', '1.0.6', {

From 3bafc18b1ec39a339ec8b80a4d0272d724b0bbb4 Mon Sep 17 00:00:00 2001
From: alberta <adrien.albert@unige.ch>
Date: Tue, 21 Mar 2023 17:52:58 +0100
Subject: [PATCH 135/601] adding easyconfigs: Bottleneck-1.3.7-foss-2022a.eb

---
 .../Bottleneck/Bottleneck-1.3.7-foss-2022a.eb | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb
new file mode 100644
index 00000000000..ddcca5a30f1
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb
@@ -0,0 +1,23 @@
+easyblock = 'PythonPackage'
+
+name = 'Bottleneck'
+version = '1.3.7'
+
+homepage = 'https://kwgoodman.github.io/bottleneck-doc'
+description = "Fast NumPy array functions written in C"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['e1467e373ad469da340ed0ff283214d6531cc08bfdca2083361a3aa6470681f8']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'

From 5ffb30987f094f6f9f9626c244924b8b412aa8ce Mon Sep 17 00:00:00 2001
From: alberta <adrien.albert@unige.ch>
Date: Tue, 21 Mar 2023 17:54:25 +0100
Subject: [PATCH 136/601] adding easyconfigs: numexpr-2.8.4-foss-2022a.eb

---
 .../n/numexpr/numexpr-2.8.4-foss-2022a.eb     | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb
new file mode 100644
index 00000000000..41f638503e2
--- /dev/null
+++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb
@@ -0,0 +1,21 @@
+name = 'numexpr'
+version = '2.8.4'
+
+homepage = 'https://numexpr.readthedocs.io/en/latest/'
+description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can.
+ It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into
+ code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a
+ compiler at runtime."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = ['0e21addd25db5f62d60d97e4380339d9c1fb2de72c88b070c279776ee6455d10']
+
+dependencies = [
+    ('Python',       '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+]
+
+moduleclass = 'math'

From fbdfe2a2e445a360f8cf7304200c9757126264c8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Mar 2023 17:57:35 +0100
Subject: [PATCH 137/601] adding easyconfigs: HTSplotter-2.11-foss-2022b.eb,
 Seaborn-0.12.2-foss-2022b.eb

---
 .../HTSplotter/HTSplotter-2.11-foss-2022b.eb  | 47 +++++++++++++++++++
 .../s/Seaborn/Seaborn-0.12.2-foss-2022b.eb    | 24 ++++++++++
 2 files changed, 71 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb

diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb
new file mode 100644
index 00000000000..00810cd3b19
--- /dev/null
+++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'HTSplotter'
+version = '2.11'
+
+homepage = 'https://github.com/CBIGR/HTSplotter'
+description = """HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro
+perturbation screens."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('matplotlib', '3.7.0'),
+    ('h5py', '3.8.0'),
+    ('Seaborn', '0.12.2'),
+    ('tqdm', '4.64.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('minio', '7.1.13', {
+        'checksums': ['8828615a20cde82df79c5a52005252ad29bb022cde25177a4a43952a04c3222c'],
+    }),
+    ('pypdf', '3.6.0', {
+        'checksums': ['7d7bd0603f4e87a7064597aa968fcf77a065b596cfbe6e5003a5b00a043db230'],
+    }),
+    ('PyPDF2', '3.0.1', {
+        'modulename': 'PyPDF2',
+        'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'],
+    }),
+    ('PyPDF3', '1.0.6', {
+        'modulename': 'PyPDF3',
+        'checksums': ['c946f3273419e37258e35e72273f49904ab15723d87a761c1115ef99799f8c5f'],
+    }),
+    (name, version, {
+        'modulename': 'HTSplotter',
+        'checksums': ['51c0cee4e8eeecfd03f32dd707e0fa433cec91abb9334ec1d28e7f82615dbe29'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb
new file mode 100644
index 00000000000..ca9fa388cb0
--- /dev/null
+++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'Seaborn'
+version = '0.12.2'
+
+homepage = 'https://seaborn.pydata.org/'
+description = """ Seaborn is a Python visualization library based on matplotlib.
+ It provides a high-level interface for drawing attractive statistical graphics. """
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['374645f36509d0dcab895cba5b47daf0586f77bfe3b36c97c607db7da5be0139']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('matplotlib', '3.7.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'bio'

From a59eaab667a3aede49b78fa9ef26846d25b45182 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 21 Mar 2023 18:14:11 +0100
Subject: [PATCH 138/601] adding easyconfigs: WIEN2k-21.1-intel-2021b.eb

---
 .../w/WIEN2k/WIEN2k-21.1-intel-2021b.eb       | 77 +++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb

diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
new file mode 100644
index 00000000000..f7adddd82b1
--- /dev/null
+++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
@@ -0,0 +1,77 @@
+name = 'WIEN2k'
+version = '21.1'
+
+homepage = 'http://www.wien2k.at/'
+description = """The program package WIEN2k allows to perform electronic structure calculations of solids
+using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave
+((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations.
+WIEN2k is an all-electron scheme including relativistic effects and has many features."""
+
+toolchain = {'name': 'intel', 'version': '2021b'}
+
+sources = ['%(name)s_%(version)s.tar']
+patches = [
+    '%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch',
+    '%(name)s-%(version)s_fix_system_stderr_redirection.patch',
+]
+checksums = [
+    '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11',  # WIEN2k_21.1.tar
+    '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84',  # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch
+    # WIEN2k-21.1_fix_system_stderr_redirection.patch
+    'cdba467b0b6f2b310c2e1e2a3e6cabe75f8fd15ee0f7c14f8ef80c7e48073bdd',
+]
+
+download_instructions = """
+WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html.
+"""
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('Perl', '5.34.0'),
+    ('DFT-D3', '3.2.0'),
+    ('ELPA', '2021.11.001'),
+    ('FFTW', '3.3.10'),
+    ('libxc', '5.1.6'),
+]
+
+osdependencies = [
+    ('glibc-devel', 'libc6-dev'), # required for libpthread.a
+    ('tcsh'),  # required by the installer
+]
+
+# remote = 'pbsssh'
+# If using a Slurm batch system it is highly recommended to use
+# 'srun -n_NP_ _EXEC_' for wien_mpirun
+wien_mpirun = 'mpirun  -np _NP_ _EXEC_'
+use_remote = False
+mpi_remote = False
+wien_granularity = True
+taskset = 'no'
+
+# Change as needed, these are the defaults
+# nmatmax = 19000
+# nume = 6000
+
+fix_perl_shebang_for = [
+    'iniel_pressure_in2reader.pl_lapw',
+    'iniel_pressure_reader.pl_lapw',
+    'setrmt_lapw',
+    'elast_setup_input.pl_lapw',
+    'bashtime2csh.pl_lapw',
+]
+
+tests = [
+    # test case 1: NaCl
+    ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']),
+    # test case 2: TiO2
+    ('TiO2',
+     '-b -numk 1000 -rkmax 7.5',
+     '-in1ef -cc 0.00001 -fc 0.5 -i 100',
+     [
+         r'^:ENE.*-4018.07',
+         r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces',
+         r'^:FGL002.*15.*total forces',
+     ]),
+]
+
+moduleclass = 'chem'

From 25e2fe2e4e0c3620dd48abcc5c0610e9e7a4767f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 21 Mar 2023 19:22:53 +0100
Subject: [PATCH 139/601] Add additional space

---
 easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
index f7adddd82b1..0bbc5bd89de 100644
--- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
+++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
@@ -35,7 +35,7 @@ dependencies = [
 ]
 
 osdependencies = [
-    ('glibc-devel', 'libc6-dev'), # required for libpthread.a
+    ('glibc-devel', 'libc6-dev'),  # required for libpthread.a
     ('tcsh'),  # required by the installer
 ]
 

From 8c9d7f6bdc7007e4581c0c7a4672a83ac0814e36 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 21 Mar 2023 19:39:09 +0100
Subject: [PATCH 140/601] Switch to older ELPA version

---
 easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
index 0bbc5bd89de..0a988032e84 100644
--- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
+++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb
@@ -29,7 +29,7 @@ dependencies = [
     ('Python', '3.9.6'),
     ('Perl', '5.34.0'),
     ('DFT-D3', '3.2.0'),
-    ('ELPA', '2021.11.001'),
+    ('ELPA', '2021.05.001'),
     ('FFTW', '3.3.10'),
     ('libxc', '5.1.6'),
 ]

From e592d753b33b82a3d115e9ad2269a8499e027828 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Mar 2023 19:41:52 +0100
Subject: [PATCH 141/601] adding easyconfigs: funannotate-1.8.13-foss-2021b.eb,
 GOATOOLS-1.3.1-foss-2021b.eb, pydot-1.4.2-GCCcore-11.2.0.eb

---
 .../funannotate-1.8.13-foss-2021b.eb          | 45 ++++++++++++++
 .../g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb   | 58 +++++++++++++++++++
 .../p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb     | 26 +++++++++
 3 files changed, 129 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb
 create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb
 create mode 100644 easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb
new file mode 100644
index 00000000000..78068a53cc2
--- /dev/null
+++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb
@@ -0,0 +1,45 @@
+easyblock = 'PythonBundle'
+
+name = 'funannotate'
+version = '1.8.13'
+
+homepage = 'https://funannotate.readthedocs.io'
+description = """funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work
+ with higher eukaryotes)"""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),
+    ('Biopython', '1.79'),
+    ('GOATOOLS', '1.3.1'),
+    ('matplotlib', '3.4.3'),
+    ('scikit-learn', '1.0.1'),
+    ('Seaborn', '0.11.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('distro', '1.8.0', {
+        'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'],
+    }),
+    ('natsort', '8.3.1', {
+        'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'],
+    }),
+    (name, version, {
+        'checksums': ['40819741bcb38ef3a410a242cc5f172cb0e0083570daddfe5807fb6bc0c3c384'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/funannotate'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb
new file mode 100644
index 00000000000..0c453259ec8
--- /dev/null
+++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb
@@ -0,0 +1,58 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+easyblock = 'PythonPackage'
+
+name = 'GOATOOLS'
+version = '1.3.1'
+
+homepage = 'https://github.com/tanghaibao/goatools'
+description = "A Python library for Gene Ontology analyses"
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+# must download sources via git to preserve .git directory,
+# since setuptools-scm is used to determine version
+sources = [{
+    'git_config': {
+        'url': 'https://github.com/tanghaibao',
+        'repo_name': 'goatools',
+        'tag': 'v%(version)s',
+        'keep_git_dir': True,
+    },
+    'filename': SOURCE_TAR_GZ,
+}]
+checksums = [None]
+
+builddependencies = [('cURL', '7.78.0')]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),
+    ('XlsxWriter', '3.0.2'),
+    ('statsmodels', '0.13.1'),
+    ('pydot', '1.4.2'),
+    ('openpyxl', '3.0.9'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"]
+
+sanity_check_paths = {
+    'files': ['bin/find_enrichment.py'],
+    'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh
+sanity_check_commands = [
+    "mkdir -p %(builddir)s",
+    "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo",
+    "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo",
+    "cd %(builddir)s && cp -a %(installdir)s/data .",
+    "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb
new file mode 100644
index 00000000000..c0f68a2a026
--- /dev/null
+++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb
@@ -0,0 +1,26 @@
+# updated: Denis Kristak (INUITS)
+easyblock = 'PythonPackage'
+
+name = 'pydot'
+version = '1.4.2'
+
+homepage = 'https://github.com/pydot/pydot'
+description = "Python interface to Graphviz's Dot language."
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d']
+
+builddependencies = [('binutils', '2.37')]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('Graphviz', '2.50.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'vis'

From 172f59b101057fce90dcfe692ca84220a69f29fe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Mar 2023 19:47:28 +0100
Subject: [PATCH 142/601] {bio}[foss/2022a] PhyloPhlAn v3.0.3, IQ-TREE
 v2.2.2.3, MUSCLE v5.1.0, trimAl v1.4.1, LSD2 v2.3 w/ Python 3.10.4

---
 .../i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb  | 57 +++++++++++++++++++
 .../l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb         | 38 +++++++++++++
 .../m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb   | 39 +++++++++++++
 .../PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb | 55 ++++++++++++++++++
 .../t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb   | 35 ++++++++++++
 5 files changed, 224 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb
 create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb
new file mode 100644
index 00000000000..0ea0821beb2
--- /dev/null
+++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb
@@ -0,0 +1,57 @@
+# Updated to v2.1.3 by
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+easyblock = 'CMakeMake'
+
+name = 'IQ-TREE'
+version = '2.2.2.3'
+
+# HTTPS is not working
+homepage = 'http://www.iqtree.org/'
+description = """Efficient phylogenomic software by maximum likelihood"""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary
+
+source_urls = ['https://github.com/iqtree/iqtree2/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'IQ-TREE-2.1.2_use_EB_LSD2.patch',
+    'IQ-TREE-2.2.1_fix-mpi.patch',
+]
+checksums = [
+    {'v2.2.2.3.tar.gz': 'fb15dfcdf63ce20f371763fff925804809f2fd5b7faaad1fb09a6f2bc7c2ba01'},
+    {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'},
+    {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Eigen', '3.4.0'),
+]
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('Boost', '1.79.0'),
+    ('LSD2', '2.3'),
+]
+
+local_conf_opts = ' -DUSE_LSD2=ON '
+configopts = [
+    '-DIQTREE_FLAGS=omp' + local_conf_opts,
+    '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts,
+]
+
+sanity_check_paths = {
+    'files': ['bin/iqtree2', 'bin/iqtree2-mpi'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "iqtree2 --help",
+    "mkdir -p $TMPDIR/{test-omp,test-mpi}",
+    "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy",
+    "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy",
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..c13e24fcc53
--- /dev/null
+++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb
@@ -0,0 +1,38 @@
+# Updated to v2.3 by
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+easyblock = 'CMakeMake'
+
+name = 'LSD2'
+version = '2.3'
+
+homepage = 'https://github.com/tothuhien/lsd2'
+description = "Least-squares methods to estimate rates and dates from phylogenies"
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'tothuhien'
+
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v.%(version)s.tar.gz']
+patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch']
+checksums = [
+    'c7819be1204ebf77e3660bba91dbd8629ba9437216814f276a11b9156dbb0649',  # v.2.3.tar.gz
+    # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch
+    '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6',
+]
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+build_shared_libs = True
+
+sanity_check_paths = {
+    'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..f11b43042ac
--- /dev/null
+++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'MakeCp'
+
+name = 'MUSCLE'
+version = '5.1.0'
+
+homepage = 'https://drive5.com/muscle/'
+description = """MUSCLE is one of the best-performing multiple alignment programs
+ according to published benchmark tests, with accuracy and speed that are consistently
+ better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users
+ learn everything they need to know about MUSCLE in a few minutes-only a handful of
+ command-line options are needed to perform common alignment tasks."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'rcedgar'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d']
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+start_dir = 'src'
+
+# Use build environment defined by EasyBuild
+prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&"
+buildopts = "CPP=${CXX} CC=${CC}"
+
+files_to_copy = [(['Linux/muscle'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/muscle'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["muscle -h"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb
new file mode 100644
index 00000000000..3cca6b971e6
--- /dev/null
+++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb
@@ -0,0 +1,55 @@
+# Contribution by
+# DeepThought, Flinders University
+# R.QIAO <rob.qiao@flinders.edu.au>
+# update to v3.0.2
+
+easyblock = 'PythonPackage'
+
+name = 'PhyloPhlAn'
+version = '3.0.3'
+
+homepage = 'https://github.com/biobakery/phylophlan'
+description = """
+PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of
+genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method
+for large-scale microbial genome characterization and phylogenetic analysis
+at multiple levels of resolution.
+"""
+
+source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags']
+sources = ['%(version)s.tar.gz']
+checksums = ['d8d0082c95d58d7b11a60c1e2214b35c1a23a65675005f1393e7647d76c6a054']
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('Biopython', '1.79'),
+    ('DendroPy', '4.5.2'),
+    ('matplotlib', '3.5.2'),
+    ('Seaborn', '0.12.1'),
+    ('FastTree', '2.1.11'),
+    ('IQ-TREE', '2.2.2.3'),
+    ('MUSCLE', '5.1.0'),
+    ('MAFFT', '7.505', '-with-extensions'),
+    ('SEPP', '4.5.1'),
+    ('trimAl', '1.4.1'),
+    ('BLAST+', '2.13.0'),
+    ('USEARCH', '11.0.667-i86linux32', '', SYSTEM),
+    ('DIAMOND', '2.1.0'),
+]
+
+use_pip = True
+download_dep_fail = True
+
+sanity_pip_check = True
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']],
+    'dirs': ['lib'],
+}
+sanity_check_commands = [('%(namelower)s', '-h')]
+
+options = {'modulename': '%(namelower)s'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..8da2ca94e6c
--- /dev/null
+++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb
@@ -0,0 +1,35 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Updated by:
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+easyblock = 'MakeCp'
+
+name = 'trimAl'
+version = '1.4.1'
+
+homepage = 'https://github.com/scapella/trimal'
+description = """EVB, FEP and LIE simulator."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'scapella'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e']
+
+builddependencies = [
+    ('binutils', '2.38'),
+
+]
+start_dir = 'source'
+
+files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/trimal', 'bin/readal', 'bin/statal'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

From 06cff2a5d5a59f6fcd37734cfd05db6102722ec6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Mar 2023 19:52:34 +0100
Subject: [PATCH 143/601] adding easyconfigs: MetaPhlAn-4.0.6-foss-2022a.eb,
 CMSeq-1.0.4-foss-2022a.eb, biom-format-2.1.14-foss-2022a.eb

---
 .../biom-format-2.1.14-foss-2022a.eb          | 47 ++++++++++++++++++
 .../c/CMSeq/CMSeq-1.0.4-foss-2022a.eb         | 37 ++++++++++++++
 .../m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb | 48 +++++++++++++++++++
 3 files changed, 132 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb
new file mode 100644
index 00000000000..e518ffc2793
--- /dev/null
+++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb
@@ -0,0 +1,47 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage:     https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::     Robert Qiao <rob.qiao@flinders.edu.au>
+# License::     Revised BSD
+#
+# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b
+##
+
+easyblock = 'PythonPackage'
+
+name = 'biom-format'
+version = '2.1.14'
+
+homepage = 'https://biom-format.org'
+description = """
+The BIOM file format (canonically pronounced biome) is designed to be
+ a general-use format for representing biological sample by observation
+ contingency tables. BIOM is a recognized standard for the Earth Microbiome
+ Project and is a Genomics Standards Consortium supported project.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c8bac94ab6aa8226c0d38af7a3341d65e5f3664b9f45ec44fdf8b5275b2f92c1']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('h5py', '3.7.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/biom'],
+    'dirs': ['lib'],
+}
+
+options = {'modulename': 'biom'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb
new file mode 100644
index 00000000000..841eb0499fc
--- /dev/null
+++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb
@@ -0,0 +1,37 @@
+# Contribution by
+# DeepThought, Flinders University
+# R.QIAO <rob.qiao@flinders.edu.au>
+
+easyblock = 'PythonPackage'
+
+name = 'CMSeq'
+version = '1.0.4'
+
+homepage = 'https://github.com/SegataLab/cmseq/'
+description = "CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['93038a6dba826e29a66df3ec8ab2b3e3872acac7af9df245e4a5a624584aca5c']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('Biopython', '1.79'),
+    ('bcbio-gff', '0.7.0'),
+    ('biom-format', '2.1.14'),
+    ('Pysam', '0.20.0'),
+    ('SAMtools', '1.16.1'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['breadth_depth.py', 'consensus.py', 'poly.py', 'polymut.py']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb
new file mode 100644
index 00000000000..a2aebcc69ea
--- /dev/null
+++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb
@@ -0,0 +1,48 @@
+# Contribution by
+# DeepThought, Flinders University
+# R.QIAO <rob.qiao@flinders.edu.au>
+
+easyblock = 'PythonBundle'
+
+name = 'MetaPhlAn'
+version = '4.0.6'
+
+homepage = 'https://github.com/biobakery/MetaPhlAn'
+description = """MetaPhlAn is a computational tool for profiling the composition
+ of microbial communities from metagenomic shotgun sequencing data """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('Biopython', '1.79'),
+    ('Pysam', '0.20.0'),
+    ('DendroPy', '4.5.2'),
+    ('CMSeq', '1.0.4'),
+    ('biom-format', '2.1.14'),
+    ('h5py', '3.7.0'),
+    ('PhyloPhlAn', '3.0.3'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('hclust2', '1.0.0', {
+        'checksums': ['9667f1d16628940aedd3d1d571b956a6f77795018e3ea4dd83f234419eb0096d'],
+    }),
+    (name, version, {
+        'checksums': ['e810d6b894ec6d0029255407f03a7dea1753ff65bde333ab34b40544cfb5553e'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/'],
+}
+
+sanity_check_commands = ["metaphlan -h"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 9f50a299b623b1e387d3524fb87560f115d56838 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 21 Mar 2023 21:44:55 +0100
Subject: [PATCH 144/601] Rename KrakenUniq-1.0.3-foss-2022a.eb to
 KrakenUniq-1.0.3-GCC-11.3.0.eb

---
 ...kenUniq-1.0.3-foss-2022a.eb => KrakenUniq-1.0.3-GCC-11.3.0.eb} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/k/KrakenUniq/{KrakenUniq-1.0.3-foss-2022a.eb => KrakenUniq-1.0.3-GCC-11.3.0.eb} (100%)

diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb
similarity index 100%
rename from easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb
rename to easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb

From 3b9c2102fc3a735bf6177f98257cb56e119452be Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 21 Mar 2023 21:50:28 +0100
Subject: [PATCH 145/601] adding easyconfigs: DiCE-ML-0.9-foss-2022a.eb

---
 .../d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb       | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb

diff --git a/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb b/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb
new file mode 100644
index 00000000000..1103677a97a
--- /dev/null
+++ b/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'DiCE-ML'
+version = '0.9'
+
+homepage = 'https://interpret.ml/DiCE'
+description = "Diverse Counterfactual Explanations (DiCE) for ML"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('h5py', '3.7.0'),
+    ('scikit-learn', '1.1.2'),
+    ('tqdm', '4.64.0'),
+]
+
+sources = ['dice_ml-%(version)s.tar.gz']
+checksums = ['0c4c2cb57f2218ba324ef2931304ab42f5f685759688a5898b0eb85b7a25b97a']
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'ai'

From 0125ffc4e948d7b59b4c7f5100af31bd5fbfad62 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 22 Mar 2023 10:11:11 +0100
Subject: [PATCH 146/601] fix preinstallopts for ravenpy extension in Raven
 easyconfig

---
 .../easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb  | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
index 82f6b075da7..0e32ebaa9e0 100644
--- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb
@@ -21,7 +21,6 @@ preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && "
 configopts = '-DRAVEN_BUILD_EXE=1 -G Ninja '
 configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python '
 
-
 dependencies = [
     ('Python', '3.9.6'),
     ('zlib', '1.2.11'),
@@ -34,15 +33,18 @@ exts_default_options = {
     'use_pip': True,
 }
 
+# inject addition CMake options to make sure that Python dependency is actually used
+local_ravenpy_preinstallopts = r"""sed -i 's|cmake_args += \["-GNinja"\]|cmake_args += \["""
+local_ravenpy_preinstallopts += r'"-GNinja", "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",'
+local_ravenpy_preinstallopts += r""" "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|' setup.py && """
+
 exts_list = [
     (name, version, {
         'modulename': 'ravenpy',
         'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'],
         'sources': ['%(version)s.tar.gz'],
         'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'],
-        'preinstallopts': r'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \
-            "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",\
-            "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|\' setup.py && '
+        'preinstallopts': local_ravenpy_preinstallopts,
     }),
 ]
 
@@ -50,7 +52,7 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 
 sanity_check_paths = {
     'files': ['bin/raven'],
-    'dirs': []
+    'dirs': [],
 }
 
 sanity_check_commands = [
@@ -58,4 +60,4 @@ sanity_check_commands = [
     "raven --help"
 ]
 
-moduleclass = "bio"
+moduleclass = 'bio'

From ed6c995e5e8adf04359c0fe4e72c37993cdedaeb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 22 Mar 2023 10:14:52 +0100
Subject: [PATCH 147/601] stick to Pysam 0.19.1 for CMSeq 1.0.4 and etaPhlAn
 4.0.6

---
 easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb         | 2 +-
 easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb
index 841eb0499fc..b16ab7d9572 100644
--- a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb
@@ -21,7 +21,7 @@ dependencies = [
     ('Biopython', '1.79'),
     ('bcbio-gff', '0.7.0'),
     ('biom-format', '2.1.14'),
-    ('Pysam', '0.20.0'),
+    ('Pysam', '0.19.1'),
     ('SAMtools', '1.16.1'),
 ]
 
diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb
index a2aebcc69ea..16e6771ac7d 100644
--- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb
@@ -17,7 +17,7 @@ dependencies = [
     ('Python', '3.10.4'),
     ('SciPy-bundle', '2022.05'),
     ('Biopython', '1.79'),
-    ('Pysam', '0.20.0'),
+    ('Pysam', '0.19.1'),
     ('DendroPy', '4.5.2'),
     ('CMSeq', '1.0.4'),
     ('biom-format', '2.1.14'),

From d08b98fcbab00dfcaccd82f96116b8bd9be877a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Wed, 22 Mar 2023 10:44:32 +0100
Subject: [PATCH 148/601] remove suffix

---
 ...11.3.0-Python-3.10.4.eb => pyparsing-3.0.9-GCCcore-11.3.0.eb} | 1 -
 1 file changed, 1 deletion(-)
 rename easybuild/easyconfigs/p/pyparsing/{pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb => pyparsing-3.0.9-GCCcore-11.3.0.eb} (95%)

diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb
similarity index 95%
rename from easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb
rename to easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb
index 9ef3f6d433b..0c8b7ea8098 100644
--- a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb
+++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb
@@ -2,7 +2,6 @@ easyblock = 'PythonPackage'
 
 name = 'pyparsing'
 version = '3.0.9'
-versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/pyparsing/pyparsing'
 description = """The pyparsing module is an alternative approach to creating and

From dd4a51ffe55d55caf9b7a66fc2dbfcbfd6ec3917 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 22 Mar 2023 17:28:06 +0100
Subject: [PATCH 149/601] CuPy: skip TestProduct tests due to badly written
 tests with float16

---
 .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
index a665a1371c4..d194347e4cd 100644
--- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
@@ -36,6 +36,8 @@ _skip_tests = [
     'tests/cupy_tests/testing_tests/test_parameterized.py',
     'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_',
     'tests/cupy_tests/fft_tests/test_fft.py',
+    # float16 has too low precision for these tests as they are written
+    'tests/cupy_tests/linalg_tests/test_product.py::TestProduct',
 ]
 _ignore_list = ' --ignore='.join(_skip_tests)
 
@@ -46,7 +48,7 @@ exts_list = [
     ('cupy', version, {
         # Must run tests here since the required version of pytest is a builddep
         # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory.
-        'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' %\
+        'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' %
                    _ignore_list,
         'testinstall': True,
         'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'],

From 6954664e67b706ae98be2019309078339c1e45f6 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 22 Mar 2023 17:34:47 +0100
Subject: [PATCH 150/601] pytest: Add comment about file system related tests
 that may fail on a shared FS.

---
 .../easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb      | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
index e8ab8e89799..8f1d64d7528 100644
--- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb
@@ -22,6 +22,11 @@ use_pip = True
 
 exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]}
 
+# Note! Some of the file system related tests may fail on shared file systems.
+# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir
+# and test_source_mtime_long_long are known to fail on GPFS
+# Build with buildpath and tmpdir set to a local file system to avoid this
+# or use --ignore-test-failures
 _skip_tests = [
     'testing/io/test_terminalwriter.py',
     'testing/test_terminal.py',

From 7d38ff546856847ae8ba9d58033f3a4ad45a91ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 22 Mar 2023 18:01:27 +0100
Subject: [PATCH 151/601] Switch bamtofastq to cargo easyblock

---
 .../bamtofastq-1.4.0-GCCcore-10.3.0.eb        | 163 +++++++++++++++++-
 1 file changed, 158 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
index db9e0c95129..987340268d8 100644
--- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
@@ -1,4 +1,4 @@
-easyblock = 'Binary'
+easyblock = 'Cargo'
 
 name = 'bamtofastq'
 version = '1.4.0'
@@ -8,6 +8,163 @@ description = """Convert 10x BAM files to the original FASTQs compatible with 10
 
 toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
 
+crates = [
+    ('anyhow', '1.0.44'),
+    ('backtrace', '0.3.61'),
+    ('addr2line', '0.16.0'),
+    ('gimli', '0.25.0'),
+    ('cfg-if', '1.0.0'),
+    ('libc', '0.2.103'),
+    ('miniz_oxide', '0.4.4'),
+    ('adler', '1.0.2'),
+    ('autocfg', '1.0.1'),
+    ('object', '0.26.2'),
+    ('memchr', '2.4.1'),
+    ('rustc-demangle', '0.1.21'),
+    ('cc', '1.0.71'),
+    ('jobserver', '0.1.24'),
+    ('libc', '0.2.103'),
+    ('backtrace', '0.3.61'),
+    ('bincode', '1.3.3'),
+    ('serde', '1.0.130'),
+    ('serde_derive', '1.0.130'),
+    ('proc-macro2', '1.0.29'),
+    ('unicode-xid', '0.2.2'),
+    ('quote', '1.0.10'),
+    ('proc-macro2', '1.0.29'),
+    ('syn', '1.0.80'),
+    ('proc-macro2', '1.0.29'),
+    ('quote', '1.0.10'),
+    ('unicode-xid', '0.2.2'),
+    ('csv', '1.1.6'),
+    ('bstr', '0.2.17'),
+    ('lazy_static', '1.4.0'),
+    ('memchr', '2.4.1'),
+    ('regex-automata', '0.1.10'),
+    ('serde', '1.0.130'),
+    ('csv-core', '0.1.10'),
+    ('memchr', '2.4.1'),
+    ('itoa', '0.4.8'),
+    ('ryu', '1.0.5'),
+    ('serde', '1.0.130'),
+    ('docopt', '1.1.1'),
+    ('lazy_static', '1.4.0'),
+    ('regex', '1.5.4'),
+    ('aho-corasick', '0.7.18'),
+    ('memchr', '2.4.1'),
+    ('memchr', '2.4.1'),
+    ('regex-syntax', '0.6.25'),
+    ('serde', '1.0.130'),
+    ('strsim', '0.10.0'),
+    ('flate2', '1.0.22'),
+    ('cfg-if', '1.0.0'),
+    ('crc32fast', '1.2.1'),
+    ('cfg-if', '1.0.0'),
+    ('libc', '0.2.103'),
+    ('libz-sys', '1.1.3'),
+    ('libc', '0.2.103'),
+    ('cc', '1.0.71'),
+    ('cmake', '0.1.45'),
+    ('cc', '1.0.71'),
+    ('pkg-config', '0.3.20'),
+    ('itertools', '0.10.1'),
+    ('either', '1.6.1'),
+    ('regex', '1.5.4'),
+    ('rust-htslib', '0.38.2'),
+    ('bio-types', '0.12.0'),
+    ('derive-new', '0.5.9'),
+    ('proc-macro2', '1.0.29'),
+    ('quote', '1.0.10'),
+    ('syn', '1.0.80'),
+    ('lazy_static', '1.4.0'),
+    ('regex', '1.5.4'),
+    ('strum_macros', '0.20.1'),
+    ('heck', '0.3.3'),
+    ('unicode-segmentation', '1.8.0'),
+    ('proc-macro2', '1.0.29'),
+    ('quote', '1.0.10'),
+    ('syn', '1.0.80'),
+    ('thiserror', '1.0.29'),
+    ('thiserror-impl', '1.0.29'),
+    ('proc-macro2', '1.0.29'),
+    ('quote', '1.0.10'),
+    ('syn', '1.0.80'),
+    ('byteorder', '1.4.3'),
+    ('custom_derive', '0.1.7'),
+    ('derive-new', '0.5.9'),
+    ('hts-sys', '2.0.2'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('libc', '0.2.103'),
+    ('cc', '1.0.71'),
+    ('pkg-config', '0.3.20'),
+    ('libdeflate-sys', '0.5.0'),
+    ('cc', '1.0.71'),
+    ('libz-sys', '1.1.3'),
+    ('lzma-sys', '0.1.17'),
+    ('libc', '0.2.103'),
+    ('cc', '1.0.71'),
+    ('pkg-config', '0.3.20'),
+    ('cc', '1.0.71'),
+    ('fs-utils', '1.1.4'),
+    ('quick-error', '1.2.3'),
+    ('glob', '0.3.0'),
+    ('ieee754', '0.2.6'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.103'),
+    ('linear-map', '1.2.0'),
+    ('newtype_derive', '0.1.6'),
+    ('rustc_version', '0.1.7'),
+    ('semver', '0.1.20'),
+    ('regex', '1.5.4'),
+    ('thiserror', '1.0.29'),
+    ('url', '2.2.2'),
+    ('form_urlencoded', '1.0.1'),
+    ('matches', '0.1.9'),
+    ('percent-encoding', '2.1.0'),
+    ('idna', '0.2.3'),
+    ('matches', '0.1.9'),
+    ('unicode-bidi', '0.3.7'),
+    ('unicode-normalization', '0.1.19'),
+    ('tinyvec', '1.5.0'),
+    ('tinyvec_macros', '0.1.0'),
+    ('matches', '0.1.9'),
+    ('percent-encoding', '2.1.0'),
+    ('serde', '1.0.130'),
+    ('serde_bytes', '0.11.5'),
+    ('serde', '1.0.130'),
+    ('serde_derive', '1.0.130'),
+    ('shardio', '0.8.1'),
+    ('anyhow', '1.0.44'),
+    ('bincode', '1.3.3'),
+    ('byteorder', '1.4.3'),
+    ('crossbeam-channel', '0.5.1'),
+    ('cfg-if', '1.0.0'),
+    ('crossbeam-utils', '0.8.5'),
+    ('cfg-if', '1.0.0'),
+    ('lazy_static', '1.4.0'),
+    ('log', '0.4.14'),
+    ('cfg-if', '1.0.0'),
+    ('lz4', '1.23.2'),
+    ('libc', '0.2.103'),
+    ('lz4-sys', '1.9.2'),
+    ('libc', '0.2.103'),
+    ('cc', '1.0.71'),
+    ('min-max-heap', '1.3.0'),
+    ('serde', '1.0.130'),
+    ('tempfile', '3.2.0'),
+    ('cfg-if', '1.0.0'),
+    ('libc', '0.2.103'),
+    ('rand', '0.8.4'),
+    ('libc', '0.2.103'),
+    ('rand_chacha', '0.3.1'),
+    ('ppv-lite86', '0.2.10'),
+    ('rand_core', '0.6.3'),
+    ('getrandom', '0.2.3'),
+    ('cfg-if', '1.0.0'),
+    ('libc', '0.2.103'),
+    ('rand_core', '0.6.3'),
+    ('remove_dir_all', '0.5.3'),
+]
 source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags']
 sources = ['v%(version)s.tar.gz']
 checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed']
@@ -20,10 +177,6 @@ builddependencies = [
 
 dependencies = [('bzip2', '1.0.8')]
 
-extract_sources = True
-
-install_cmd = "cargo build --release && cargo install --root %(installdir)s --path ."
-
 sanity_check_paths = {
     'files': ['bin/%(namelower)s'],
     'dirs': [],

From 363522fe490064d8f810b9bee3c9f92937dfbe1d Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 24 Mar 2023 12:38:28 +0100
Subject: [PATCH 152/601] add missing OpenJPEG dependency for recent GDAL
 versions

---
 .../g/GDAL/GDAL-3.5.0-foss-2022a.eb           |  1 +
 .../g/GDAL/GDAL-3.6.2-foss-2022b.eb           |  1 +
 .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb | 42 +++++++++++++++++++
 3 files changed, 44 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb
index 6cf3d77cc5c..6babf890be5 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb
@@ -43,6 +43,7 @@ dependencies = [
     ('SciPy-bundle', '2022.05'),
     ('HDF5', '1.12.2'),
     ('HDF', '4.2.15'),
+    ('OpenJPEG', '2.5.0'),
 ]
 
 preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && "
diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
index 01346b45e3a..7e3c17c850f 100644
--- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb
@@ -56,6 +56,7 @@ dependencies = [
     ('Brunsli', '0.1'),
     ('Qhull', '2020.2'),
     ('LERC', '4.0.0'),
+    ('OpenJPEG', '2.5.0'),
 ]
 
 # common configopts for static, shared library builds
diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..1c0e9a28999
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenJPEG'
+version = '2.5.0'
+
+homepage = 'https://www.openjpeg.org/'
+description = """OpenJPEG is an open-source JPEG 2000 codec written in
+ C language. It has been developed in order to promote the use of JPEG 2000,
+ a still-image compression standard from the Joint Photographic Experts Group
+ (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as
+ a JPEG 2000 Reference Software."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/uclouvain/%(namelower)s/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc.
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('libpng', '1.6.38'),
+    ('LibTIFF', '4.4.0'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/opj_compress',
+        'bin/opj_decompress',
+        'bin/opj_dump',
+        'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h',
+        'lib/libopenjp2.%s' % SHLIB_EXT
+    ],
+    'dirs': ['bin', 'include', 'lib'],
+}
+
+moduleclass = 'lib'

From 22b845071723e7a6ad786e6549edd531ba05ab5b Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Fri, 24 Mar 2023 13:32:56 +0100
Subject: [PATCH 153/601] Added easyconfig for cppzmq

---
 .../c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb       | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb
new file mode 100644
index 00000000000..57f913bc462
--- /dev/null
+++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'CMakeMake'
+
+name = 'cppzmq'
+version = '4.9.0'
+
+homepage = 'https://github.com/zeromq/cppzmq'
+description = "cppzmq is a C++ binding for libzmq."
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/zeromq/%(name)s/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['3fdf5b100206953f674c94d40599bdb3ea255244dcc42fab0d75855ee3645581']
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+    ('ZeroMQ', '4.3.4'),
+]
+
+sanity_check_paths = {
+    'files': ['include/zmq.hpp'],
+    'dirs': ['include','lib'],
+}
+
+moduleclass = 'lib'

From 372a2086b3b22b815236711909b31b322940f812 Mon Sep 17 00:00:00 2001
From: lenocil <lenocil@strw.leidenuniv.nl>
Date: Fri, 24 Mar 2023 13:35:20 +0100
Subject: [PATCH 154/601] Added whitespace

---
 easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb
index 57f913bc462..e78d4d15a99 100644
--- a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb
@@ -19,7 +19,7 @@ builddependencies = [
 
 sanity_check_paths = {
     'files': ['include/zmq.hpp'],
-    'dirs': ['include','lib'],
+    'dirs': ['include', 'lib'],
 }
 
 moduleclass = 'lib'

From a5b6658beb342b119fa62c9ca88a0d944a4bf46a Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 25 Mar 2023 11:10:12 +0000
Subject: [PATCH 155/601] cleanup

---
 .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
index 352ea582005..1b5f6973977 100644
--- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
+++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
@@ -10,9 +10,6 @@ description = """Bioconductor provides tools for the analysis and coprehension
 
 toolchain = {'name': 'foss', 'version': '2022b'}
 
-# lpsymphony fails to build with pkgconf, so stick to pkg-config
-# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286
-# builddependencies = [('pkg-config', '0.29.2')]
 builddependencies = [('pkgconf', '1.9.3')]
 
 dependencies = [
@@ -46,7 +43,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s
 
 # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends
 # !! order of packages is important !!
-# packages updated on 7th Nov 2022
+# packages updated on 18th March 2023
 exts_list = [
     ('BiocGenerics', '0.44.0', {
         'checksums': ['8518e462c1ef103ab059d059d871afc444e48f56fe6b3afdb60dc1abf6c9b09d'],
@@ -442,12 +439,7 @@ exts_list = [
         'checksums': ['6eba6fdd689fdd5d18fde3ffe4aa64ad4af5bfdc8977b8038d297fb46ed10515'],
     }),
     ('dada2', '1.26.0', {
-        'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'],
-        'checksums': [
-            {'dada2_1.26.0.tar.gz': '6c9ee66abfa2e21096b8a3669346a445ee051308d9773f2d9e6e4ea230c1aeb1'},
-            {'dada2-1.16.0-remove-sse-on-aarch64.patch':
-             'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935'},
-        ],
+        'checksums': ['6c9ee66abfa2e21096b8a3669346a445ee051308d9773f2d9e6e4ea230c1aeb1'],
     }),
     ('LEA', '3.10.2', {
         'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'],

From 5ca7aa3a5c7a5a517a81d450ce736b07c89f482b Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Mon, 27 Mar 2023 12:31:01 +0200
Subject: [PATCH 156/601] Add AlphaFold and deps

---
 .../AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb | 167 ++++++++++++++++++
 .../h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb  |  90 ++++++++++
 .../k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb   |  27 +++
 .../OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb |  62 +++++++
 ...enMM-7.5.1_fix_Doxygen_compatibility.patch |  24 +++
 5 files changed, 370 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb
 create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb
 create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..a84e24f20d3
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,167 @@
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold'
+version = '2.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://deepmind.com/research/case-studies/alphafold'
+description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    # required for installing dm-tree
+    ('Bazel', '5.1.1'),
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('TensorFlow', '2.11.0', versionsuffix),
+    ('Biopython', '1.79'),
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.3.2'),
+    ('Kalign', '3.3.5'),
+    ('jax', '0.3.14', versionsuffix),  # also provides absl-py
+    ('UCX-CUDA', '1.12.1', versionsuffix),
+    ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM),
+    ('NCCL', '2.12.12', versionsuffix),
+    # AlphaFold doesn't work with latest OpenMM, so have to use v7.5.1
+    ('OpenMM', '7.5.1', '-DeepMind-patch'),
+]
+
+# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
+# see docker/Dockerfile in AlphaFold repository
+local_scp_commit = '7102c6'
+
+components = [
+    (name, version, {
+        'easyblock': 'PythonPackage',
+        'source_urls': [
+            'https://github.com/deepmind/alphafold/archive/refs/tags/',
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [
+            {
+                'download_filename': 'v%(version)s.tar.gz',
+                'filename': SOURCE_TAR_GZ,
+            },
+            {
+                'download_filename': 'stereo_chemical_props.txt',
+                'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+                'extract_cmd': "cp %s .",
+            },
+        ],
+        'patches': [
+            'AlphaFold-2.0.0_fix-packages.patch',
+            'AlphaFold-2.3.0_data-dep-paths.patch',
+            'AlphaFold-2.0.0_n-cpu.patch',
+            'AlphaFold-2.1.0_fix-scp-path.patch',
+            'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+        ],
+        'checksums': [
+            '52055a0b4bf194ae0e1960e6391e501490f82274c975e01c1ff0e353a1cd59d9',  # v2.3.0.tar.gz
+            '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
+            '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
+            '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0',  # AlphaFold-2.3.0_data-dep-paths.patch
+            'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
+            '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f',  # AlphaFold-2.1.0_fix-scp-path.patch
+            '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac',  # AlphaFold-2.0.1_setup_rm_tfcpu.patch
+
+        ],
+        'start_dir': 'alphafold-%(version)s',
+        'use_pip': True,
+    }),
+]
+
+use_pip = True
+
+exts_list = [
+    ('PDBFixer', '1.8.1', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'],
+    }),
+    ('toolz', '0.12.0', {
+        'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
+    }),
+    ('chex', '0.1.6', {
+        'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'],
+    }),
+    ('tabulate', '0.9.0', {
+        'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'],
+    }),
+    ('jmp', '0.0.4', {
+        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+    }),
+    ('dm-haiku', '0.0.9', {
+        'modulename': 'haiku',
+        'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'],
+    }),
+    ('dm-tree', '0.1.8', {
+        'modulename': 'tree',
+        'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'],
+    }),
+    ('websocket-client', '1.5.1', {
+        'modulename': 'websocket',
+        'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'],
+    }),
+    ('docker', '6.0.1', {
+        'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'],
+    }),
+    ('immutabledict', '2.2.3', {
+        'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    # run_alphafold.py script is missing a shebang...
+    "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
+    "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
+    "chmod a+x %(installdir)s/bin/run_alphafold*.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/",
+    "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
+    # run tests for run_alphafold.py script;
+    # shouldn't do this in sanity check to avoid breaking use of --module-only
+    "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
+    "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py",
+]
+
+sanity_check_paths = {
+    'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
+}
+
+sanity_check_commands = [
+    "pdbfixer --help",
+    "python -m simtk.testInstallation",
+    "python -c 'import alphafold'",
+    "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
+]
+
+sanity_pip_check = True
+
+# these allow to make predictions on proteins that would typically be too long to fit into GPU memory;
+# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py
+modextravars = {
+    'TF_FORCE_UNIFIED_MEMORY': '1',
+    'XLA_PYTHON_CLIENT_MEM_FRACTION': '3',
+    # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs',  # please adapt
+    'OPENMM_RELAX': 'CUDA'  # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb
new file mode 100644
index 00000000000..1e8dd76e708
--- /dev/null
+++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb
@@ -0,0 +1,90 @@
+##
+# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+# Updated to use gompi-2020b toolchain:
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'CMakeMake'
+
+name = 'HH-suite'
+version = '3.3.0'
+
+homepage = 'https://github.com/soedinglab/hh-suite'
+description = """The HH-suite is an open-source software package
+ for sensitive protein sequence searching based on the pairwise
+ alignment of hidden Markov models (HMMs)."""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://github.com/soedinglab/hh-suite/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Perl', '5.34.1'),
+    ('Python', '3.10.4'),
+]
+
+_binaries_help = [
+    'cstranslate', 'cstranslate_mpi', 'hhalign', 'hhalign_mpi', 'hhalign_omp', 'hhconsensus',
+    'hhfilter', 'hhmake'
+]
+
+_binaries_h = [
+    'a3m_database_extract', 'a3m_database_filter', 'a3m_database_reduce', 'a3m_extract', 'a3m_reduce',
+    'hhblits', 'hhblits_ca3m', 'hhblits_mpi', 'hhblits_omp', 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp'
+]
+
+_binaries_version = ['ffindex_build', 'ffindex_from_fasta', 'ffindex_modify']
+
+_binaries_v = ['ffindex_from_fasta_with_split']
+
+_binaries_helpless = [
+    'ffindex_apply', 'ffindex_apply_mpi', 'ffindex_get',
+    'ffindex_order', 'ffindex_reduce', 'ffindex_unpack'
+]
+
+_scriptfiles = ['hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py']
+
+fix_perl_shebang_for = ['scripts/*pl']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _binaries_help] +
+             ['bin/%s' % x for x in _binaries_h] +
+             ['bin/%s' % x for x in _binaries_version] +
+             ['bin/%s' % x for x in _binaries_v] +
+             ['bin/%s' % x for x in _binaries_helpless] +
+             ['scripts/%s' % y for y in _scriptfiles],
+    'dirs': ['data', 'scripts']
+}
+
+sanity_check_commands = ['%s --help' % x for x in _binaries_help]
+sanity_check_commands += ['%s -h' % x for x in _binaries_h]
+sanity_check_commands += ['%s --version' % x for x in _binaries_version]
+sanity_check_commands += ['%s -v' % x for x in _binaries_v]
+sanity_check_commands += ['%s 2>&1 | grep USAGE' % x for x in _binaries_helpless]
+
+modextrapaths = {
+    'PATH': 'scripts',
+    'PERL5LIB': 'scripts',
+}
+
+modextravars = {
+    'HHLIB': '%(installdir)s',
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..3dfcd8a4213
--- /dev/null
+++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb
@@ -0,0 +1,27 @@
+# Contribution from the NIHR Biomedical Research Centre
+easyblock = 'CMakeMake'
+
+name = 'Kalign'
+version = '3.3.5'
+
+homepage = 'https://github.com/TimoLassmann/kalign'
+description = "Kalign is a fast multiple sequence alignment program for biological sequences."
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/TimoLassmann/kalign/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['75f3a127d2a9eef1eafd931fb0785736eb3f82826be506e7edd00daf1ba26212']
+
+builddependencies = [
+    ('CMake', '3.23.1')
+]
+
+sanity_check_paths = {
+    'files': ['bin/kalign'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["kalign --help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb
new file mode 100644
index 00000000000..e1e07a395fb
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb
@@ -0,0 +1,62 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenMM'
+version = '7.5.1'
+versionsuffix = '-DeepMind-patch'
+
+homepage = 'https://openmm.org'
+description = "OpenMM is a toolkit for molecular simulation."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/openmm/openmm/archive/']
+sources = ['%(version)s.tar.gz']
+patches = [
+    ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'),
+    'OpenMM-7.5.1_fix_Doxygen_compatibility.patch',
+]
+checksums = [
+    'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7',
+    '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6',
+    '86664f02a1ca70e02b977102798d5e1ba333d1543914951af42706a461f1564c',
+]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('Doxygen', '1.9.4'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('SWIG', '4.0.2'),
+]
+
+runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """
+
+preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '
+preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && '
+
+# required to install the python API
+installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s'
+
+local_python_path = 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg'
+
+sanity_check_paths = {
+    'files': [
+        'lib/libOpenMM.%s' % SHLIB_EXT,
+        local_python_path + '/simtk/openmm/openmm.py',
+    ],
+    'dirs': []
+}
+
+sanity_check_commands = ["python -m simtk.testInstallation"]
+
+modextrapaths = {
+    'PYTHONPATH': local_python_path,
+    'OPENMM_INCLUDE_PATH': 'include',
+    'OPENMM_LIB_PATH': 'lib',
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch
new file mode 100644
index 00000000000..1cf2ffa4a56
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch
@@ -0,0 +1,24 @@
+# Fixes compatibility issue with Doxygen >= 1.9.2
+# See: https://github.com/openmm/openmm/issues/3317 and https://github.com/openmm/openmm/pull/3336
+# Author: maxim-masterov (SURF)
+
+diff -Nru openmm-7.5.1.orig/wrappers/generateWrappers.py openmm-7.5.1/wrappers/generateWrappers.py
+--- openmm-7.5.1.orig/wrappers/generateWrappers.py	2023-03-24 11:11:39.911916000 +0100
++++ openmm-7.5.1/wrappers/generateWrappers.py	2023-03-24 11:12:29.971967239 +0100
+@@ -82,6 +82,7 @@
+                             'const std::vector<std::tuple<int, int, double> >& OpenMM::NoseHooverIntegrator::getAllThermostatedPairs',
+                             'virtual void OpenMM::NoseHooverIntegrator::stateChanged'
+                            ] 
++        self.skipMethods = [s.replace(' ', '') for s in self.skipMethods]
+         self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
+         self.nodeByID={}
+ 
+@@ -132,7 +133,7 @@
+         for section in findNodes(classNode, "sectiondef", kind="public-static-func")+findNodes(classNode, "sectiondef", kind="public-func"):
+             for memberNode in findNodes(section, "memberdef", kind="function", prot="public"):
+                 methodDefinition = getText("definition", memberNode)
+-                if methodDefinition in self.skipMethods:
++                if methodDefinition.replace(' ', '') in self.skipMethods:
+                     continue
+                 methodList.append(memberNode)
+         return methodList

From ceb5300493f57c0a998d3b133c457eeb3110254e Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Mon, 27 Mar 2023 17:49:22 +0200
Subject: [PATCH 157/601] Update to AlphaFold-2.3.1

---
 ...AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb} | 10 ++--
 ...ixer-1.8.1_roll_back_to_openmm_1.5.1.patch | 50 +++++++++++++++++++
 2 files changed, 57 insertions(+), 3 deletions(-)
 rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb => AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb} (94%)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
similarity index 94%
rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb
rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
index a84e24f20d3..dfec7d642c9 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'AlphaFold'
-version = '2.3.0'
+version = '2.3.1'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://deepmind.com/research/case-studies/alphafold'
@@ -63,7 +63,7 @@ components = [
             'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
         ],
         'checksums': [
-            '52055a0b4bf194ae0e1960e6391e501490f82274c975e01c1ff0e353a1cd59d9',  # v2.3.0.tar.gz
+            '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a',  # v2.3.1.tar.gz
             '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
             '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
             '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0',  # AlphaFold-2.3.0_data-dep-paths.patch
@@ -83,7 +83,11 @@ exts_list = [
     ('PDBFixer', '1.8.1', {
         'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'],
+        'patches': ['%(namelower)s-%(version)s_roll_back_to_openmm_1.5.1.patch'],
+        'checksums': [
+            'd50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595',
+            'b24abffa3e1b5066a6f3bbfd0d3bb14043f3518357e26cb35dad3fae06b866d1',
+        ],
     }),
     ('toolz', '0.12.0', {
         'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
diff --git a/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch b/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch
new file mode 100644
index 00000000000..c78f2aef75f
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch
@@ -0,0 +1,50 @@
+# Roll back to OpenMM v1.5.1, as AlphaFold-2.3 doesn't support more recent versions.
+# This patch is based on the following PR: https://github.com/openmm/pdbfixer/pull/223/files
+# Author: maxim-masterov (SURF)
+
+diff -Nru pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py pdbfixer-1.8.1/pdbfixer/pdbfixer.py
+--- pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py	2023-03-27 17:28:53.564306000 +0200
++++ pdbfixer-1.8.1/pdbfixer/pdbfixer.py	2023-03-27 17:42:24.093931265 +0200
+@@ -32,18 +32,18 @@
+ __author__ = "Peter Eastman"
+ __version__ = "1.7"
+ 
+-import openmm as mm
+-import openmm.app as app
+-import openmm.unit as unit
+-from openmm.app.internal.pdbstructure import PdbStructure
+-from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
+-from openmm.app.element import hydrogen, oxygen
+-from openmm.app.forcefield import NonbondedGenerator
++import simtk.openmm as mm
++import simtk.openmm.app as app
++import simtk.unit as unit
++from simtk.openmm.app.internal.pdbstructure import PdbStructure
++from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
++from simtk.openmm.app.element import hydrogen, oxygen
++from simtk.openmm.app.forcefield import NonbondedGenerator
+ 
+ # Support Cythonized functions in OpenMM 7.3
+ # and also implementations in older versions.
+ try:
+-    from openmm.app.internal import compiled
++    from simtk.openmm.app.internal import compiled
+     matchResidue = compiled.matchResidueToTemplate
+ except ImportError:
+     matchResidue = app.forcefield._matchResidue
+diff -Nru pdbfixer-1.8.1.orig/pdbfixer/ui.py pdbfixer-1.8.1/pdbfixer/ui.py
+--- pdbfixer-1.8.1.orig/pdbfixer/ui.py	2023-03-27 17:28:53.583267000 +0200
++++ pdbfixer-1.8.1/pdbfixer/ui.py	2023-03-27 17:42:32.915332264 +0200
+@@ -6,9 +6,9 @@
+ import sys
+ from math import sqrt
+ 
+-import openmm.app as app
+-import openmm.unit as unit
+-from openmm.vec3 import Vec3
++import simtk.openmm.app as app
++import simtk.unit as unit
++from simtk.openmm.vec3 import Vec3
+ 
+ from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat
+ from . import uiserver

From 3e5714404911ee265b517c17105c66148639659a Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Mon, 27 Mar 2023 17:50:20 +0200
Subject: [PATCH 158/601] Add missing binutils

---
 easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb
index 3dfcd8a4213..fda9c28356f 100644
--- a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb
@@ -14,7 +14,8 @@ sources = ['v%(version)s.tar.gz']
 checksums = ['75f3a127d2a9eef1eafd931fb0785736eb3f82826be506e7edd00daf1ba26212']
 
 builddependencies = [
-    ('CMake', '3.23.1')
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
 ]
 
 sanity_check_paths = {

From 2f6ef9830bbbe226d052882c6203b931c1ded327 Mon Sep 17 00:00:00 2001
From: iotaka <edoardo.dilorenzo@gmail.com>
Date: Mon, 27 Mar 2023 18:34:48 +0200
Subject: [PATCH 159/601] Update Cantera-2.6.0-foss-2022a.eb

---
 .../easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb      | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb
index bb14dcff6b1..5507e6a57bc 100644
--- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb
@@ -2,6 +2,7 @@ easyblock = 'SCons'
 
 name = 'Cantera'
 version = '2.6.0'
+versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/Cantera/cantera'
 description = """Chemical kinetics, thermodynamics, and transport tool suite"""
@@ -15,6 +16,7 @@ checksums = ['7273622ea76a53373cee820f939613b15eea3dd83db6e1b127c5ed043f77dc5b']
 
 dependencies = [
     ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
     ('Boost', '1.79.0'),
     ('SUNDIALS', '6.3.0'),
     ('yaml-cpp', '0.7.0'),
@@ -28,9 +30,8 @@ builddependencies = [
 ]
 
 local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" '
-# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR '
-# local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib'
-# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib'
+local_common_opts += 'blas_lapack_libs=flexiblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR '
+local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib'
 buildopts = 'build ' + local_common_opts
 # tests hang, so disable them for now
 # runtest = 'test ' + local_common_opts

From ace6576c541d23a0ebf8f8feb62ace86b2b64689 Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Mon, 27 Mar 2023 18:51:06 +0200
Subject: [PATCH 160/601] adding CASPR easyconfig + deps'

---
 .../c/CASPR/CASPR-20200730-foss-2022a.eb      | 39 ++++++++++++++++++
 .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb        | 34 +---------------
 .../m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb     | 36 +++++++++++++++++
 .../v/vispr/vispr-0.4.14-foss-2022a.eb        | 40 +++++++++++++++++++
 .../vispr_fix_pandas_version_change.patch     | 13 ++++++
 5 files changed, 130 insertions(+), 32 deletions(-)
 create mode 100644 easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch

diff --git a/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb b/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb
new file mode 100644
index 00000000000..c32f29ed00e
--- /dev/null
+++ b/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb
@@ -0,0 +1,39 @@
+# Author: Denis Kristak (Inuits)
+
+easyblock = 'Tarball'
+
+name = 'CASPR'
+version = '20200730'
+local_commit = 'b74fde2'
+
+homepage = 'https://judithbergada.github.io/CASPR'
+description = """Running CASPR is extremely easy and convenient to analyze CRIPR-Cas9 screens using pgRNAs."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/judithbergada/CASPR/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['96cd3a8fd8f1d8cddf798f07bff46c1048ab9343aa40c31d3430f1e58703f0ac']
+
+dependencies = [
+    ('FastQC', '0.11.9', '-Java-11', SYSTEM),
+    ('cutadapt', '4.2'),
+    ('FASTX-Toolkit', '0.0.14'),
+    ('STAR', '2.7.10b'),
+    ('SAMtools', '1.16.1'),
+    ('vispr', '0.4.14'),
+    ('R', '4.2.1'),
+]
+
+modextrapaths = {
+    'PATH': 'source/',
+}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['source'],
+}
+
+sanity_check_commands = ["CASPR --help 2>&1 | grep 'Usage: CASPR'"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
index 8589f7ecedc..67d8cb141e8 100644
--- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
@@ -8,6 +8,8 @@
 #
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+#
+# Updated: Denis Kristak (Inuits)
 ##
 
 easyblock = 'Bundle'
@@ -24,11 +26,6 @@ toolchainopts = {'pic': True}
 
 default_easyblock = 'ConfigureMake'
 
-dependencies = [
-    ('GDGraph', '1.56'),
-    ('Perl', '5.34.1'),
-]
-
 components = [
     ('libgtextutils', '0.7', {
         'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'],
@@ -50,23 +47,6 @@ components = [
     }),
 ]
 
-exts_defaultclass = 'PerlModule'
-exts_filter = ("perldoc -lm %(ext_name)s ", "")
-
-exts_list = [
-    ('PerlIO::gzip', '0.20', {
-        'source_tmpl': 'PerlIO-gzip-0.20.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'],
-        'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'],
-    }),
-]
-
-fix_perl_shebang_for = ['bin/*.pl']
-
-modextrapaths = {
-    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'
-}
-
 sanity_check_paths = {
     'files':
         ['bin/fastx_%s' % x for x in
@@ -82,14 +62,4 @@ sanity_check_paths = {
     'dirs': []
 }
 
-sanity_check_commands = [
-    'fasta_clipping_histogram.pl',
-    'fasta_formatter -h',
-    'fastq_masker -h | grep "FASTX Toolkit %(version)s"',
-    'fastq_quality_boxplot_graph.sh',
-    'fastx_barcode_splitter.pl --help | grep "Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008"',
-    'fastx_clipper -h | grep "FASTX Toolkit %(version)s"',
-    'fastx_nucleotide_distribution_graph.sh',
-]
-
 moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb
new file mode 100644
index 00000000000..cc54713c3c6
--- /dev/null
+++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb
@@ -0,0 +1,36 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+# Updated: Denis Kristak (Inuits)
+easyblock = 'PythonPackage'
+
+name = 'MAGeCK'
+version = '0.5.9.4'
+
+homepage = "https://sourceforge.net/p/mageck/wiki/Home/"
+description = """Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify
+ important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed
+ by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated
+ by Wei Li lab from Children's National Medical Center."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+]
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['42875b308f2d9ee38f083fb1020d7d48fca29e2100fdb09ced1969b738b8c939']
+
+# Remove the shipped mageckGSEA and RRA binaries so that the Python install will build them
+# This avoids RPATH problems (see #15082)
+preinstallopts = "rm bin/{mageckGSEA,RRA} && "
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+sanity_check_commands = ["cd %(builddir)s/%(namelower)s-%(version)s/demo/demo1 && ./run.sh"] + [
+    "%s -h" % x for x in ['mageck', 'mageckGSEA']]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
new file mode 100644
index 00000000000..855cc5ee79b
--- /dev/null
+++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
@@ -0,0 +1,40 @@
+# Author: Denis Kristak (Inuits)
+
+easyblock = 'PythonPackage'
+
+name = 'vispr'
+version = '0.4.14'
+
+homepage = 'https://pypi.org/project/vispr/'
+
+description = """
+VISPR - A visualization framework for CRISPR data.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = ['%(name)s-%(version)s.tar.gz']
+patches = ['vispr_fix_pandas_version_change.patch']
+checksums = [
+    {'vispr-0.4.14.tar.gz': 'dc2cf6ac9c8930b0f1f1b3a2b7f57bfae180b2ac3674060123fd2d7fe10ccd82'},
+    {'vispr_fix_pandas_version_change.patch': '406c78092f1b06114602d37eb216ce24e1206b52461d0fc4270971ab80f10529'},
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Flask', '2.2.2'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('scikit-learn', '1.1.2'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/vispr'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch b/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch
new file mode 100644
index 00000000000..05275dcd59c
--- /dev/null
+++ b/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch
@@ -0,0 +1,13 @@
+# with more recent versions of Pandas, the imported error was moved to `pandas.errors`
+diff -ruN vispr-0.4.14_orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py
+--- vispr-0.4.14_orig/vispr/results/rna.py	2023-03-24 13:10:57.148839548 +0000
++++ vispr-0.4.14/vispr/results/rna.py	2023-03-24 13:11:14.032660055 +0000
+@@ -11,7 +11,7 @@
+ 
+ from flask import render_template
+ import pandas as pd
+-from pandas.io.common import EmptyDataError
++from pandas.errors import EmptyDataError
+ import numpy as np
+ from sklearn.decomposition import PCA
+ from scipy.cluster.hierarchy import average, leaves_list, dendrogram

From e04de5c7a2b9555128304492c2aa09aeeaae83ab Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <Balazs.Hajgato@UGent.be>
Date: Tue, 28 Mar 2023 08:47:52 +0200
Subject: [PATCH 161/601] Fix CodAn bin/* executable permissions for all users

---
 easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb
index 5d220aff850..ab50f6642f7 100644
--- a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb
+++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb
@@ -27,7 +27,7 @@ install_cmd = "cp -r %(builddir)s/* %(installdir)s/ && "
 install_cmd += "tar -xf %(installdir)s/%(name)s-%(version)s/CodAn.tar.gz && "
 install_cmd += "mkdir %(installdir)s/bin && "
 install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && "
-install_cmd += "chmod u+rwx %(installdir)s/bin/* "
+install_cmd += "chmod u+rwx,go+x %(installdir)s/bin/* "
 
 sanity_check_paths = {
     'files': ['bin/%(namelower)s.py'],

From f12401eb9d23661cb31756f57473f15146513802 Mon Sep 17 00:00:00 2001
From: iotaka <edoardo.dilorenzo@gmail.com>
Date: Tue, 28 Mar 2023 08:56:31 +0200
Subject: [PATCH 162/601] Update Cantera-2.6.0-foss-2022a.eb

---
 easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb
index 5507e6a57bc..2b8fbc5a70c 100644
--- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb
@@ -2,7 +2,6 @@ easyblock = 'SCons'
 
 name = 'Cantera'
 version = '2.6.0'
-versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/Cantera/cantera'
 description = """Chemical kinetics, thermodynamics, and transport tool suite"""

From 94c8d7d891bef982b18a11bae132105ebc7a8e04 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <Balazs.Hajgato@UGent.be>
Date: Tue, 28 Mar 2023 09:04:56 +0200
Subject: [PATCH 163/601] Add CodAn bin/* read permissions for all users

---
 easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb
index ab50f6642f7..636bef3b8e8 100644
--- a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb
+++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb
@@ -27,7 +27,7 @@ install_cmd = "cp -r %(builddir)s/* %(installdir)s/ && "
 install_cmd += "tar -xf %(installdir)s/%(name)s-%(version)s/CodAn.tar.gz && "
 install_cmd += "mkdir %(installdir)s/bin && "
 install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && "
-install_cmd += "chmod u+rwx,go+x %(installdir)s/bin/* "
+install_cmd += "chmod u+rwx,go+rx %(installdir)s/bin/* "
 
 sanity_check_paths = {
     'files': ['bin/%(namelower)s.py'],

From 3e6e9bbeaf63230d43b10475a8bb110303270fe5 Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 28 Mar 2023 11:36:08 +0200
Subject: [PATCH 164/601] Add OpenMM-7.7.0

---
 .../AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb |  13 +-
 ...phaFold-2.3.1_switch_to_openmm_7.7.0.patch | 240 ++++++++++++++++++
 ...ixer-1.8.1_roll_back_to_openmm_1.5.1.patch |  50 ----
 .../OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb |  62 -----
 ...enMM-7.5.1_fix_Doxygen_compatibility.patch |  24 --
 5 files changed, 245 insertions(+), 144 deletions(-)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch
 delete mode 100644 easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch
 delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb
 delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
index dfec7d642c9..cb5cfdb2a9d 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
@@ -29,8 +29,7 @@ dependencies = [
     ('UCX-CUDA', '1.12.1', versionsuffix),
     ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM),
     ('NCCL', '2.12.12', versionsuffix),
-    # AlphaFold doesn't work with latest OpenMM, so have to use v7.5.1
-    ('OpenMM', '7.5.1', '-DeepMind-patch'),
+    ('OpenMM', '7.7.0'),
 ]
 
 # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
@@ -61,6 +60,7 @@ components = [
             'AlphaFold-2.0.0_n-cpu.patch',
             'AlphaFold-2.1.0_fix-scp-path.patch',
             'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+            'AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch',
         ],
         'checksums': [
             '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a',  # v2.3.1.tar.gz
@@ -70,6 +70,7 @@ components = [
             'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
             '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f',  # AlphaFold-2.1.0_fix-scp-path.patch
             '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac',  # AlphaFold-2.0.1_setup_rm_tfcpu.patch
+            'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec',  # AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch
 
         ],
         'start_dir': 'alphafold-%(version)s',
@@ -83,11 +84,7 @@ exts_list = [
     ('PDBFixer', '1.8.1', {
         'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'patches': ['%(namelower)s-%(version)s_roll_back_to_openmm_1.5.1.patch'],
-        'checksums': [
-            'd50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595',
-            'b24abffa3e1b5066a6f3bbfd0d3bb14043f3518357e26cb35dad3fae06b866d1',
-        ],
+        'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'],
     }),
     ('toolz', '0.12.0', {
         'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
@@ -152,7 +149,7 @@ sanity_check_paths = {
 
 sanity_check_commands = [
     "pdbfixer --help",
-    "python -m simtk.testInstallation",
+    "python -m openmm.testInstallation",
     "python -c 'import alphafold'",
     "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
 ]
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch
new file mode 100644
index 00000000000..ff3aa457201
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch
@@ -0,0 +1,240 @@
+# Add compatibility with OpenMM-7.7.0
+# The patch is based on the recipe from https://github.com/deepmind/alphafold/issues/404
+# Author: maxim-masterov (SURF)
+
+diff -Nru alphafold-2.3.1.orig/alphafold/relax/amber_minimize.py alphafold-2.3.1/alphafold/relax/amber_minimize.py
+--- alphafold-2.3.1.orig/alphafold/relax/amber_minimize.py	2023-03-28 10:58:07.126241000 +0200
++++ alphafold-2.3.1/alphafold/relax/amber_minimize.py	2023-03-28 11:24:17.380332000 +0200
+@@ -27,10 +27,10 @@
+ import ml_collections
+ import numpy as np
+ import jax
+-from simtk import openmm
+-from simtk import unit
+-from simtk.openmm import app as openmm_app
+-from simtk.openmm.app.internal.pdbstructure import PdbStructure
++from openmm import *
++from openmm import unit
++from openmm import app as openmm_app
++from openmm.app.internal.pdbstructure import PdbStructure
+ 
+ 
+ ENERGY = unit.kilocalories_per_mole
+@@ -47,7 +47,7 @@
+ 
+ 
+ def _add_restraints(
+-    system: openmm.System,
++    system: System,
+     reference_pdb: openmm_app.PDBFile,
+     stiffness: unit.Unit,
+     rset: str,
+diff -Nru alphafold-2.3.1.orig/alphafold/relax/cleanup.py alphafold-2.3.1/alphafold/relax/cleanup.py
+--- alphafold-2.3.1.orig/alphafold/relax/cleanup.py	2023-03-28 10:58:07.126999000 +0200
++++ alphafold-2.3.1/alphafold/relax/cleanup.py	2023-03-28 11:03:20.689464000 +0200
+@@ -20,8 +20,8 @@
+ import io
+ 
+ import pdbfixer
+-from simtk.openmm import app
+-from simtk.openmm.app import element
++from openmm import app
++from openmm.app import element
+ 
+ 
+ def fix_pdb(pdbfile, alterations_info):
+diff -Nru alphafold-2.3.1.orig/alphafold/relax/cleanup_test.py alphafold-2.3.1/alphafold/relax/cleanup_test.py
+--- alphafold-2.3.1.orig/alphafold/relax/cleanup_test.py	2023-03-28 10:58:07.127710000 +0200
++++ alphafold-2.3.1/alphafold/relax/cleanup_test.py	2023-03-28 11:03:14.772207000 +0200
+@@ -17,7 +17,7 @@
+ 
+ from absl.testing import absltest
+ from alphafold.relax import cleanup
+-from simtk.openmm.app.internal import pdbstructure
++from openmm.app.internal import pdbstructure
+ 
+ 
+ def _pdb_to_structure(pdb_str):
+diff -Nru alphafold-2.3.1.orig/docker/Dockerfile alphafold-2.3.1/docker/Dockerfile
+--- alphafold-2.3.1.orig/docker/Dockerfile	2023-03-28 10:58:07.081432000 +0200
++++ alphafold-2.3.1/docker/Dockerfile	2023-03-28 11:04:09.608354000 +0200
+@@ -76,7 +76,6 @@
+ 
+ # Apply OpenMM patch.
+ WORKDIR /opt/conda/lib/python3.8/site-packages
+-RUN patch -p0 < /app/alphafold/docker/openmm.patch
+ 
+ # Add SETUID bit to the ldconfig binary so that non-root users can run it.
+ RUN chmod u+s /sbin/ldconfig.real
+diff -Nru alphafold-2.3.1.orig/notebooks/AlphaFold.ipynb alphafold-2.3.1/notebooks/AlphaFold.ipynb
+--- alphafold-2.3.1.orig/notebooks/AlphaFold.ipynb	2023-03-28 10:58:07.092241000 +0200
++++ alphafold-2.3.1/notebooks/AlphaFold.ipynb	2023-03-28 11:04:51.464351000 +0200
+@@ -103,16 +103,16 @@
+         "      %shell rm -rf /opt/conda\n",
+         "      %shell wget -q -P /tmp \\\n",
+         "        https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \\\n",
+-        "          \u0026\u0026 bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n",
+-        "          \u0026\u0026 rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n",
++        "          && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n",
++        "          && rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n",
+         "      pbar.update(9)\n",
+         "\n",
+         "      PATH=%env PATH\n",
+         "      %env PATH=/opt/conda/bin:{PATH}\n",
+         "      %shell conda install -qy conda==4.13.0 \\\n",
+-        "          \u0026\u0026 conda install -qy -c conda-forge \\\n",
++        "          && conda install -qy -c conda-forge \\\n",
+         "            python=3.8 \\\n",
+-        "            openmm=7.5.1 \\\n",
++        "            openmm=7.7.0 \\\n",
+         "            pdbfixer\n",
+         "      pbar.update(80)\n",
+         "\n",
+@@ -161,8 +161,7 @@
+         "      pbar.update(10)\n",
+         "\n",
+         "      # Apply OpenMM patch.\n",
+-        "      %shell pushd /opt/conda/lib/python3.8/site-packages/ \u0026\u0026 \\\n",
+-        "          patch -p0 \u003c /content/alphafold/docker/openmm.patch \u0026\u0026 \\\n",
++        "      %shell pushd /opt/conda/lib/python3.8/site-packages/ && \\\n",
+         "          popd\n",
+         "\n",
+         "      # Make sure stereo_chemical_props.txt is in all locations where it could be searched for.\n",
+@@ -186,9 +185,9 @@
+         "\n",
+         "import jax\n",
+         "if jax.local_devices()[0].platform == 'tpu':\n",
+-        "  raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n",
++        "  raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n",
+         "elif jax.local_devices()[0].platform == 'cpu':\n",
+-        "  raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n",
++        "  raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n",
+         "else:\n",
+         "  print(f'Running with {jax.local_devices()[0].device_kind} GPU')\n",
+         "\n",
+@@ -206,7 +205,7 @@
+       "source": [
+         "## Making a prediction\n",
+         "\n",
+-        "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ \u003e _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n",
++        "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ > _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n",
+         "\n",
+         "Note that the search against databases and the actual prediction can take some time, from minutes to hours, depending on the length of the protein and what type of GPU you are allocated by Colab (see FAQ below)."
+       ]
+@@ -298,21 +297,21 @@
+         "\n",
+         "# Check whether total length exceeds limit.\n",
+         "total_sequence_length = sum([len(seq) for seq in sequences])\n",
+-        "if total_sequence_length \u003e MAX_LENGTH:\n",
++        "if total_sequence_length > MAX_LENGTH:\n",
+         "  raise ValueError('The total sequence length is too long: '\n",
+         "                   f'{total_sequence_length}, while the maximum is '\n",
+         "                   f'{MAX_LENGTH}.')\n",
+         "\n",
+         "# Check whether we exceed the monomer limit.\n",
+         "if model_type_to_use == ModelType.MONOMER:\n",
+-        "  if len(sequences[0]) \u003e MAX_MONOMER_MODEL_LENGTH:\n",
++        "  if len(sequences[0]) > MAX_MONOMER_MODEL_LENGTH:\n",
+         "    raise ValueError(\n",
+         "        f'Input sequence is too long: {len(sequences[0])} amino acids, while '\n",
+         "        f'the maximum for the monomer model is {MAX_MONOMER_MODEL_LENGTH}. You may '\n",
+         "        'be able to run this sequence with the multimer model by selecting the '\n",
+         "        'use_multimer_model_for_monomers checkbox above.')\n",
+         "    \n",
+-        "if total_sequence_length \u003e MAX_VALIDATED_LENGTH:\n",
++        "if total_sequence_length > MAX_VALIDATED_LENGTH:\n",
+         "  print('WARNING: The accuracy of the system has not been fully validated '\n",
+         "        'above 3000 residues, and you may experience long running times or '\n",
+         "        f'run out of memory. Total sequence length is {total_sequence_length} '\n",
+@@ -407,7 +406,7 @@
+         "]\n",
+         "\n",
+         "# Search UniProt and construct the all_seq features only for heteromers, not homomers.\n",
+-        "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n",
++        "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n",
+         "  MSA_DATABASES.extend([\n",
+         "      # Swiss-Prot and TrEMBL are concatenated together as UniProt.\n",
+         "      {'db_name': 'uniprot',\n",
+@@ -441,7 +440,7 @@
+         "  for sequence_index, sequence in enumerate(sorted(set(sequences)), 1):\n",
+         "    fasta_path = f'target_{sequence_index:02d}.fasta'\n",
+         "    with open(fasta_path, 'wt') as f:\n",
+-        "      f.write(f'\u003equery\\n{sequence}')\n",
++        "      f.write(f'>query\\n{sequence}')\n",
+         "    sequence_to_fasta_path[sequence] = fasta_path\n",
+         "\n",
+         "  # Run the search against chunks of genetic databases (since the genetic\n",
+@@ -502,7 +501,7 @@
+         "      num_templates=0, num_res=len(sequence)))\n",
+         "\n",
+         "  # Construct the all_seq features only for heteromers, not homomers.\n",
+-        "  if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n",
++        "  if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n",
+         "    valid_feats = msa_pairing.MSA_FEATURES + (\n",
+         "        'msa_species_identifiers',\n",
+         "    )\n",
+@@ -662,7 +661,7 @@
+         "banded_b_factors = []\n",
+         "for plddt in plddts[best_model_name]:\n",
+         "  for idx, (min_val, max_val, _) in enumerate(PLDDT_BANDS):\n",
+-        "    if plddt \u003e= min_val and plddt \u003c= max_val:\n",
++        "    if plddt >= min_val and plddt <= max_val:\n",
+         "      banded_b_factors.append(idx)\n",
+         "      break\n",
+         "banded_b_factors = np.array(banded_b_factors)[:, None] * final_atom_mask\n",
+@@ -675,14 +674,14 @@
+         "  f.write(relaxed_pdb)\n",
+         "\n",
+         "\n",
+-        "# --- Visualise the prediction \u0026 confidence ---\n",
++        "# --- Visualise the prediction & confidence ---\n",
+         "show_sidechains = True\n",
+         "def plot_plddt_legend():\n",
+         "  \"\"\"Plots the legend for pLDDT.\"\"\"\n",
+-        "  thresh = ['Very low (pLDDT \u003c 50)',\n",
+-        "            'Low (70 \u003e pLDDT \u003e 50)',\n",
+-        "            'Confident (90 \u003e pLDDT \u003e 70)',\n",
+-        "            'Very high (pLDDT \u003e 90)']\n",
++        "  thresh = ['Very low (pLDDT < 50)',\n",
++        "            'Low (70 > pLDDT > 50)',\n",
++        "            'Confident (90 > pLDDT > 70)',\n",
++        "            'Very high (pLDDT > 90)']\n",
+         "\n",
+         "  colors = [x[2] for x in PLDDT_BANDS]\n",
+         "\n",
+@@ -796,13 +795,13 @@
+         "id": "jeb2z8DIA4om"
+       },
+       "source": [
+-        "## FAQ \u0026 Troubleshooting\n",
++        "## FAQ & Troubleshooting\n",
+         "\n",
+         "\n",
+         "*   How do I get a predicted protein structure for my protein?\n",
+         "    *   Click on the _Connect_ button on the top right to get started.\n",
+         "    *   Paste the amino acid sequence of your protein (without any headers) into the “Enter the amino acid sequence to fold”.\n",
+-        "    *   Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ \u003e _Run all._ Make sure you run all 5 cells in order.\n",
++        "    *   Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ > _Run all._ Make sure you run all 5 cells in order.\n",
+         "    *   The predicted protein structure will be downloaded once all cells have been executed. Note: This can take minutes to hours - see below.\n",
+         "*   How long will this take?\n",
+         "    *   Downloading the AlphaFold source code can take up to a few minutes.\n",
+@@ -811,8 +810,8 @@
+         "    *   Running AlphaFold and generating the prediction can take minutes to hours, depending on the length of your protein and on which GPU-type Colab has assigned you.\n",
+         "*   My Colab no longer seems to be doing anything, what should I do?\n",
+         "    *   Some steps may take minutes to hours to complete.\n",
+-        "    *   If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ \u003e _Restart runtime_.\n",
+-        "    *   If this doesn’t help, try resetting your Colab runtime via _Runtime_ \u003e _Factory reset runtime_.\n",
++        "    *   If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ > _Restart runtime_.\n",
++        "    *   If this doesn’t help, try resetting your Colab runtime via _Runtime_ > _Factory reset runtime_.\n",
+         "*   How does this compare to the open-source version of AlphaFold?\n",
+         "    *   This Colab version of AlphaFold searches a selected portion of the BFD dataset and currently doesn’t use templates, so its accuracy is reduced in comparison to the full version of AlphaFold that is described in the [AlphaFold paper](https://doi.org/10.1038/s41586-021-03819-2) and [Github repo](https://github.com/deepmind/alphafold/) (the full version is available via the inference script).\n",
+         "*   What is a Colab?\n",
+@@ -821,7 +820,7 @@
+         "    *   The resources allocated to your Colab vary. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n",
+         "    *   You can execute the Colab nonetheless.\n",
+         "*   I received an error “Colab CPU runtime not supported” or “No GPU/TPU found”, what do I do?\n",
+-        "    *   Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ \u003e _Change runtime type_ \u003e _Hardware accelerator_ \u003e _GPU_.\n",
++        "    *   Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ > _Change runtime type_ > _Hardware accelerator_ > _GPU_.\n",
+         "    *   The type of GPU allocated to your Colab varies. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n",
+         "    *   If you receive “Cannot connect to GPU backend”, you can try again later to see if Colab allocates you a GPU.\n",
+         "    *   [Colab Pro](https://colab.research.google.com/signup) offers priority access to GPUs.\n",
diff --git a/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch b/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch
deleted file mode 100644
index c78f2aef75f..00000000000
--- a/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-# Roll back to OpenMM v1.5.1, as AlphaFold-2.3 doesn't support more recent versions.
-# This patch is based on the following PR: https://github.com/openmm/pdbfixer/pull/223/files
-# Author: maxim-masterov (SURF)
-
-diff -Nru pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py pdbfixer-1.8.1/pdbfixer/pdbfixer.py
---- pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py	2023-03-27 17:28:53.564306000 +0200
-+++ pdbfixer-1.8.1/pdbfixer/pdbfixer.py	2023-03-27 17:42:24.093931265 +0200
-@@ -32,18 +32,18 @@
- __author__ = "Peter Eastman"
- __version__ = "1.7"
- 
--import openmm as mm
--import openmm.app as app
--import openmm.unit as unit
--from openmm.app.internal.pdbstructure import PdbStructure
--from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
--from openmm.app.element import hydrogen, oxygen
--from openmm.app.forcefield import NonbondedGenerator
-+import simtk.openmm as mm
-+import simtk.openmm.app as app
-+import simtk.unit as unit
-+from simtk.openmm.app.internal.pdbstructure import PdbStructure
-+from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
-+from simtk.openmm.app.element import hydrogen, oxygen
-+from simtk.openmm.app.forcefield import NonbondedGenerator
- 
- # Support Cythonized functions in OpenMM 7.3
- # and also implementations in older versions.
- try:
--    from openmm.app.internal import compiled
-+    from simtk.openmm.app.internal import compiled
-     matchResidue = compiled.matchResidueToTemplate
- except ImportError:
-     matchResidue = app.forcefield._matchResidue
-diff -Nru pdbfixer-1.8.1.orig/pdbfixer/ui.py pdbfixer-1.8.1/pdbfixer/ui.py
---- pdbfixer-1.8.1.orig/pdbfixer/ui.py	2023-03-27 17:28:53.583267000 +0200
-+++ pdbfixer-1.8.1/pdbfixer/ui.py	2023-03-27 17:42:32.915332264 +0200
-@@ -6,9 +6,9 @@
- import sys
- from math import sqrt
- 
--import openmm.app as app
--import openmm.unit as unit
--from openmm.vec3 import Vec3
-+import simtk.openmm.app as app
-+import simtk.unit as unit
-+from simtk.openmm.vec3 import Vec3
- 
- from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat
- from . import uiserver
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb
deleted file mode 100644
index e1e07a395fb..00000000000
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb
+++ /dev/null
@@ -1,62 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'OpenMM'
-version = '7.5.1'
-versionsuffix = '-DeepMind-patch'
-
-homepage = 'https://openmm.org'
-description = "OpenMM is a toolkit for molecular simulation."
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-toolchainopts = {'opt': True}
-
-source_urls = ['https://github.com/openmm/openmm/archive/']
-sources = ['%(version)s.tar.gz']
-patches = [
-    ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'),
-    'OpenMM-7.5.1_fix_Doxygen_compatibility.patch',
-]
-checksums = [
-    'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7',
-    '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6',
-    '86664f02a1ca70e02b977102798d5e1ba333d1543914951af42706a461f1564c',
-]
-
-builddependencies = [
-    ('CMake', '3.23.1'),
-    ('Doxygen', '1.9.4'),
-]
-
-dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('SWIG', '4.0.2'),
-]
-
-runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """
-
-preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '
-preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && '
-
-# required to install the python API
-installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s'
-
-local_python_path = 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg'
-
-sanity_check_paths = {
-    'files': [
-        'lib/libOpenMM.%s' % SHLIB_EXT,
-        local_python_path + '/simtk/openmm/openmm.py',
-    ],
-    'dirs': []
-}
-
-sanity_check_commands = ["python -m simtk.testInstallation"]
-
-modextrapaths = {
-    'PYTHONPATH': local_python_path,
-    'OPENMM_INCLUDE_PATH': 'include',
-    'OPENMM_LIB_PATH': 'lib',
-}
-
-moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch
deleted file mode 100644
index 1cf2ffa4a56..00000000000
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-# Fixes compatibility issue with Doxygen >= 1.9.2
-# See: https://github.com/openmm/openmm/issues/3317 and https://github.com/openmm/openmm/pull/3336
-# Author: maxim-masterov (SURF)
-
-diff -Nru openmm-7.5.1.orig/wrappers/generateWrappers.py openmm-7.5.1/wrappers/generateWrappers.py
---- openmm-7.5.1.orig/wrappers/generateWrappers.py	2023-03-24 11:11:39.911916000 +0100
-+++ openmm-7.5.1/wrappers/generateWrappers.py	2023-03-24 11:12:29.971967239 +0100
-@@ -82,6 +82,7 @@
-                             'const std::vector<std::tuple<int, int, double> >& OpenMM::NoseHooverIntegrator::getAllThermostatedPairs',
-                             'virtual void OpenMM::NoseHooverIntegrator::stateChanged'
-                            ] 
-+        self.skipMethods = [s.replace(' ', '') for s in self.skipMethods]
-         self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
-         self.nodeByID={}
- 
-@@ -132,7 +133,7 @@
-         for section in findNodes(classNode, "sectiondef", kind="public-static-func")+findNodes(classNode, "sectiondef", kind="public-func"):
-             for memberNode in findNodes(section, "memberdef", kind="function", prot="public"):
-                 methodDefinition = getText("definition", memberNode)
--                if methodDefinition in self.skipMethods:
-+                if methodDefinition.replace(' ', '') in self.skipMethods:
-                     continue
-                 methodList.append(memberNode)
-         return methodList

From 25466dc4baf0d3b0742f33246404ec10d15e235e Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 28 Mar 2023 11:56:49 +0200
Subject: [PATCH 165/601] Switch to OpenMM-8.0.0

---
 .../AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb |  7 ++-
 ...=> AlphaFold-2.3.1_use_openmm_7.7.0.patch} |  0
 .../o/OpenMM/OpenMM-8.0.0-foss-2022a.eb       | 60 +++++++++++++++++++
 3 files changed, 64 insertions(+), 3 deletions(-)
 rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch => AlphaFold-2.3.1_use_openmm_7.7.0.patch} (100%)
 create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
index cb5cfdb2a9d..6818ca92607 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
@@ -29,7 +29,7 @@ dependencies = [
     ('UCX-CUDA', '1.12.1', versionsuffix),
     ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM),
     ('NCCL', '2.12.12', versionsuffix),
-    ('OpenMM', '7.7.0'),
+    ('OpenMM', '8.0.0'),
 ]
 
 # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
@@ -60,7 +60,7 @@ components = [
             'AlphaFold-2.0.0_n-cpu.patch',
             'AlphaFold-2.1.0_fix-scp-path.patch',
             'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
-            'AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch',
+            'AlphaFold-2.3.1_use_openmm_7.7.0.patch',
         ],
         'checksums': [
             '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a',  # v2.3.1.tar.gz
@@ -70,7 +70,8 @@ components = [
             'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
             '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f',  # AlphaFold-2.1.0_fix-scp-path.patch
             '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac',  # AlphaFold-2.0.1_setup_rm_tfcpu.patch
-            'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec',  # AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch
+            # AlphaFold-2.3.1_use_openmm_7.7.0.patch
+            'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec',
 
         ],
         'start_dir': 'alphafold-%(version)s',
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_use_openmm_7.7.0.patch
similarity index 100%
rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch
rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_use_openmm_7.7.0.patch
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
new file mode 100644
index 00000000000..47d3bdbfaf5
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
@@ -0,0 +1,60 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# Update to 7.5.1
+# J. Sassmannshausen / GSTT
+
+easyblock = 'CMakeMake'
+
+name = 'OpenMM'
+version = '8.0.0'
+
+homepage = 'https://openmm.org'
+description = "OpenMM is a toolkit for molecular simulation."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/openmm/openmm/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('Doxygen', '1.9.4'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('SWIG', '4.0.2'),
+]
+
+pretestopts = " CTEST_OUTPUT_ON_FAILURE=1"
+local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)"
+runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern
+
+preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '
+preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && '
+
+# required to install the python API
+installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['lib/libOpenMM.%s' % SHLIB_EXT],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+sanity_check_commands = [
+    "python -c 'import simtk.openmm'",
+    "python -m openmm.testInstallation",
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg',
+    'OPENMM_INCLUDE_PATH': 'include',
+    'OPENMM_LIB_PATH': 'lib',
+}
+
+moduleclass = 'bio'

From 2109fa1f9d4008aca31d59611d7447209866fb10 Mon Sep 17 00:00:00 2001
From: iotaka <edoardo.dilorenzo@gmail.com>
Date: Tue, 28 Mar 2023 11:57:56 +0200
Subject: [PATCH 166/601] Update
 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb         | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb
index 36bfe330597..cb07437830e 100644
--- a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb
@@ -21,4 +21,11 @@ sanity_check_paths = {
     'dirs': ['share']
 }
 
+sanity_check_commands = [
+    'dumpsexp --version',
+    'hmac256 --version',
+    'mpicalc --version',
+    'libgcrypt-config --version | grep "%(version)s"',
+]
+
 moduleclass = 'system'

From ba5b2fbbf84342c96361b3e24924e019e81d0ffd Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 28 Mar 2023 11:59:27 +0100
Subject: [PATCH 167/601] adding easyconfigs: FHI-aims-221103-intel-2022a.eb

---
 .../f/FHI-aims/FHI-aims-221103-intel-2022a.eb | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb

diff --git a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb
new file mode 100644
index 00000000000..7e9bb34bb35
--- /dev/null
+++ b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb
@@ -0,0 +1,57 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Authors::   Dugan Witherick (University of Warwick)
+# Updated to 210716_3
+# J. Sassmannshausen (Imperial College London/UK)
+##
+easyblock = 'CMakeMake'
+
+name = 'FHI-aims'
+version = '221103'
+
+homepage = 'https://fhi-aims.org/'
+description = """FHI-aims is an efficient, accurate all-electron,
+full-potential electronic structure code package for computational molecular
+and materials science (non-periodic and periodic systems). The code supports
+DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is
+particularly efficient for molecular systems and nanostructures, while
+maintaining high numerical accuracy for all production tasks. Production
+calculations handle up to several thousand atoms and can efficiently use (ten)
+thousands of cores. 
+"""
+
+toolchain = {'name': 'intel', 'version': '2022a'}
+toolchainopts = {'opt': True, 'precise': True}
+
+download_instructions = """
+The source code must be downloaded manually from the FHI-aims club
+(https://fhi-aims.org/get-the-code-menu/login).
+Access to the FHI-aims club requires a valid license and registration.
+Details on available license options and how to register to access
+FHI-aims club may be found at:
+https://fhi-aims.org/get-the-code-menu/get-the-code """
+
+sources = ['%(namelower)s.%(version)s.tgz']
+checksums = ['1905147a15968b6b719a4f5d9495a958df648d3ccee58f5012734be5d6727749']
+
+builddependencies = [('CMake', '3.24.3')]
+
+configopts = ' -DCMAKE_Fortran_COMPILER="$MPIF90" '
+configopts += ' -DLIBS="mkl_scalapack_lp64 mkl_blacs_intelmpi_lp64 mkl_intel_lp64 mkl_sequential mkl_core" '
+configopts += ' -DLIB_PATHS="$CMAKE_LIBRARY_PATH" '
+configopts += ' -DCMAKE_C_FLAGS="$CFLAGS -ip" '
+configopts += ' -DCMAKE_Fortran_FLAGS="$FFLAGS -ip" '
+configopts += ' -DFortran_MIN_FLAGS="-O0 -fp-model precise" '
+configopts += ' -DTARGET_NAME="aims.x" '
+
+postinstallcmds = ["cp -ar %(builddir)s/%(namelower)s.%(version)s/{CHANGELOG.md,doc,external} %(installdir)s/",
+                   "cp -ar %(builddir)s/%(namelower)s.%(version)s/{regression_tests,species_defaults} %(installdir)s/",
+                   "cp -ar %(builddir)s/%(namelower)s.%(version)s/{testcases,utilities} %(installdir)s/"]
+
+sanity_check_paths = {
+    'files': ['bin/aims.x'],
+    'dirs': [],
+}
+
+moduleclass = 'chem'

From aaeb397e61933ef58652645181dca4429665f024 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Tue, 28 Mar 2023 12:12:29 +0100
Subject: [PATCH 168/601] adding easyconfigs: zsh-5.9.eb

---
 easybuild/easyconfigs/z/zsh/zsh-5.9.eb | 31 ++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/z/zsh/zsh-5.9.eb

diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
new file mode 100644
index 00000000000..574b12cb58d
--- /dev/null
+++ b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'zsh'
+version = '5.9'
+
+homepage = 'https://www.zsh.org/'
+description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language."
+
+toolchain = SYSTEM
+
+source_urls = ['https://prdownloads.sourceforge.net/%(namelower)s']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5']
+
+osdependencies = [
+    ('ncurses-devel', 'ncurses-dev'),
+]
+
+configopts = '--with-tcsetpgrp'  # needed to build in non-login shells
+
+modextrapaths = {'FPATH': 'share/zsh/%(version)s/functions'}
+
+sanity_check_paths = {
+    'files': ['bin/zsh'],
+    'dirs': ['lib/zsh/%(version)s', 'share'],
+}
+
+# optionally make this module sticky (lmod only):
+# modluafooter = 'add_property("lmod", "sticky")'
+
+moduleclass = 'tools'

From 264bb2e2e6cdf18e4897137b87f0a87698f10bad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 28 Mar 2023 13:22:14 +0200
Subject: [PATCH 169/601] adding easyconfigs: Bismark-0.24.0-GCC-11.3.0.eb

---
 .../b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb    | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb
new file mode 100644
index 00000000000..29cad67bb97
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb
@@ -0,0 +1,41 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2013-2014 The Cyprus Institute
+# Authors:: Thekla Loizou <t.loizou@cyi.ac.cy>
+# License:: MIT/GPL
+#
+# Updated to 0.23.1
+# J. Sassmannshausen NHS/GSTT
+
+easyblock = 'Tarball'
+
+name = 'Bismark'
+version = '0.24.0'
+
+homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/'
+description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['dd58957bd6eac44f3a6e74e9a5ef69c8d19da0e0b64feb7d019a994fe6087d7d']
+
+dependencies = [
+    ('Perl', '5.34.1'),
+    ('Bowtie2', '2.4.5'),
+    ('SAMtools', '1.16.1'),
+]
+
+sanity_check_commands = ['bismark --help']
+
+sanity_check_paths = {
+    'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation',
+              'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'],
+    'dirs': [],
+}
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'

From a199ed3fc968894362b6d6b0b340ef9721083071 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 28 Mar 2023 14:37:51 +0200
Subject: [PATCH 170/601] adding easyconfigs:
 Trim_Galore-0.6.10-GCCcore-11.3.0.eb

---
 .../Trim_Galore-0.6.10-GCCcore-11.3.0.eb      | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..0779ba13c45
--- /dev/null
+++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb
@@ -0,0 +1,46 @@
+# Contribution from the Crick HPC team
+# uploaded by J. Sassmannshausen
+# Updated to version 0.6.2: Pavel Grochal (INUITS)
+# Updated to version 0.6.5: Alex Domingo (VUB)
+# Updated to version 0.6.7 by J. Sassmannshausen NHS/GSTT
+
+easyblock = 'Tarball'
+
+name = 'Trim_Galore'
+version = '0.6.10'
+
+homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/'
+description = """Trim Galore! is a wrapper script to automate quality and adapter
+trimming as well as quality control, with some added functionality to remove biased
+methylation positions for RRBS sequence files (for directional, non-directional 
+(or paired-end) sequencing)."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['3a4e414fc658d6eb4356f1572351204e8475a9d7dc79f6798270b57d35bda017']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Java', '11', '', SYSTEM),
+    ('pigz', '2.7'),
+    ('Perl', '5.34.1'),
+    ('cutadapt', '4.2'),
+    ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM),
+]
+
+postinstallcmds = [
+    "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s",
+]
+
+fix_perl_shebang_for = ['bin/%(namelower)s']
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = [('%(namelower)s', '-v')]
+
+moduleclass = 'bio'

From 3a3162bb81152192f37effe35923b2033e8bf8e4 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 Mar 2023 15:46:14 +0200
Subject: [PATCH 171/601] fix ipython/traitlets#727 in IPython v8.5.0 by
 upgrading to v5.2.1.post0

---
 .../easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb
index 57bf257cf0c..1d65c07e244 100644
--- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb
@@ -38,8 +38,9 @@ exts_list = [
     ('prompt_toolkit', '3.0.31', {
         'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'],
     }),
-    ('traitlets', '5.2.0', {
-        'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'],
+    ('traitlets', '5.2.1.post0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['f44b708d33d98b0addb40c29d148a761f44af740603a8fd0e2f8b5b27cf0f087'],
     }),
     ('parso', '0.8.3', {
         'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'],

From cbe2516915792512bbad3a1853715a7a27f7a190 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 Mar 2023 15:46:53 +0200
Subject: [PATCH 172/601] fix ipywidgets and jupyterlab_widgets in IPython
 v8.5.0

---
 .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb    | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb
index 1d65c07e244..138f1ab5d11 100644
--- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb
@@ -24,6 +24,10 @@ dependencies = [
 
 use_pip = True
 
+# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them
+# use the versions published in a single release commit instead of blindly pushing to last available version,
+# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/c5fac25d17a93faf7bea66f5d103c605a9f19ddb
+
 exts_list = [
     ('ipython_genutils', '0.2.0', {
         'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'],
@@ -127,8 +131,8 @@ exts_list = [
     ('prometheus_client', '0.11.0', {
         'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'],
     }),
-    ('ipywidgets', '7.6.3', {
-        'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'],
+    ('ipywidgets', '7.7.4', {
+        'checksums': ['e2cca1f95b4b8e96e5c2c6ac7cfebacafb924a473df94a243a5e68b7b23172c7'],
     }),
     ('deprecation', '2.1.0', {
         'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'],
@@ -139,8 +143,8 @@ exts_list = [
     ('jupyterlab_pygments', '0.1.2', {
         'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'],
     }),
-    ('jupyterlab_widgets', '3.0.3', {
-        'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'],
+    ('jupyterlab_widgets', '1.1.3', {
+        'checksums': ['5285a4316e13f9a6512cb80a0cfec5aafa2c336097ae077a07a60c145f2154fc'],
     }),
     ('argon2-cffi', '20.1.0', {
         'modulename': 'argon2',
@@ -149,8 +153,8 @@ exts_list = [
     ('notebook', '6.4.0', {
         'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'],
     }),
-    ('widgetsnbextension', '3.5.1', {
-        'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'],
+    ('widgetsnbextension', '3.6.3', {
+        'checksums': ['28cb103f3066a6fdd6fd63264dd2a9709266c351a9a5c4a50a0bfd5ae2557b46'],
     }),
     ('matplotlib-inline', '0.1.2', {
         'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'],

From 674b4fa2e7ace347b0c266c971a58daf611669b2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 28 Mar 2023 16:11:50 +0200
Subject: [PATCH 173/601] adding easyconfigs: ipympl-0.9.3-foss-2022a.eb

---
 .../i/ipympl/ipympl-0.9.3-foss-2022a.eb       | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb

diff --git a/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb
new file mode 100644
index 00000000000..0d3dd0f948f
--- /dev/null
+++ b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'ipympl'
+version = '0.9.3'
+
+homepage = 'https://matplotlib.org/ipympl'
+description = """Leveraging the Jupyter interactive widgets framework, ipympl enables the
+interactive features of matplotlib in the Jupyter notebook and in JupyterLab.
+Besides, the figure canvas element is a proper Jupyter interactive widget which
+can be positioned in interactive widget layouts.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('JupyterLab', '3.5.0'),
+    ('matplotlib', '3.5.2'),
+    ('Pillow', '9.1.1'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['d113cd55891bafe9b27ef99b6dd111a87beb6bb2ae550c404292272103be8013'],
+    }),
+]
+
+modextrapaths = {
+    'JUPYTER_PATH': 'share/jupyter',
+    'JUPYTER_CONFIG_PATH': 'etc/jupyter',
+}
+
+moduleclass = 'tools'

From 2a6cf60ffe014fd66d8abeffd27b21b406896e6a Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Tue, 28 Mar 2023 16:34:04 +0200
Subject: [PATCH 174/601] adding easyconfigs:
 OpenFOAM-10-foss-2022a-20230119.eb

---
 .../OpenFOAM-10-foss-2022a-20230119.eb        | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
new file mode 100644
index 00000000000..5205f1afc3c
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
@@ -0,0 +1,39 @@
+name = 'OpenFOAM'
+
+version = '10'
+_version_patch = '20230119'
+versionsuffix = '-%s' % _version_patch
+
+homepage = 'https://www.openfoam.org/'
+description = """OpenFOAM is a free, open source CFD software package.
+ OpenFOAM has an extensive range of features to solve anything from complex fluid flows
+ involving chemical reactions, turbulence and heat transfer,
+ to solid dynamics and electromagnetics."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
+sources = ['%s.tar.gz' % _version_patch]
+patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch']
+checksums = [
+    {'20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'},
+    {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'},
+]
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('CMake', '3.23.1'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('ncurses', '6.3'),
+    # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes)
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '7.0.1'),
+    ('CGAL', '4.14.3'),
+    ('ParaView', '5.10.1', '-mpi'),
+    ('gnuplot', '5.4.4'),
+]
+
+moduleclass = 'cae'

From e1affca4304fd32799393b941bace3c20d8bc83f Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Tue, 28 Mar 2023 16:52:18 +0200
Subject: [PATCH 175/601] rename tarball on download

---
 .../o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb          | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
index 5205f1afc3c..f9ebf346635 100644
--- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
+++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb
@@ -13,10 +13,13 @@ description = """OpenFOAM is a free, open source CFD software package.
 toolchain = {'name': 'foss', 'version': '2022a'}
 
 source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive']
-sources = ['%s.tar.gz' % _version_patch]
+sources = [{
+    'download_filename': '%s.tar.gz' % _version_patch,
+    'filename': 'OpenFOAM-%(version)s%(versionsuffix)s.tar.gz',
+}]
 patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch']
 checksums = [
-    {'20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'},
+    {'OpenFOAM-10-20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'},
     {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'},
 ]
 

From 96b9068ee75245e73385afe7e044a60abb1e77ab Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Tue, 28 Mar 2023 15:55:09 +0100
Subject: [PATCH 176/601] disable test_native_mha test that fails on broadwell

---
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb          | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
index c77bc6a7b31..ed0747fc18c 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -141,6 +141,8 @@ excluded_tests = {
         # Those 2 abort on some machines. Skip for now
         'distributed/fsdp/test_fsdp_input',
         'distributed/fsdp/test_fsdp_mixed_precision',
+        # failing on broadwell
+        'test_native_mha'
     ]
 }
 

From c5b84219861281f6207d008ec1b7069375743c70 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 28 Mar 2023 17:03:52 +0200
Subject: [PATCH 177/601] Update
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb

---
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb         | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
index ed0747fc18c..9db805c8a42 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -141,6 +141,9 @@ excluded_tests = {
         # Those 2 abort on some machines. Skip for now
         'distributed/fsdp/test_fsdp_input',
         'distributed/fsdp/test_fsdp_mixed_precision',
+        # Produces a single test failure on some systems
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/fsdp/test_fsdp_core',
         # failing on broadwell
         'test_native_mha'
     ]

From cac561517c2ffb6bc7b8c38e9b58e29f5c99bab3 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 28 Mar 2023 17:03:59 +0200
Subject: [PATCH 178/601] Update
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb

---
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb           | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
index 9db805c8a42..7d0cc431687 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -145,6 +145,7 @@ excluded_tests = {
         # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
         'distributed/fsdp/test_fsdp_core',
         # failing on broadwell
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
         'test_native_mha'
     ]
 }

From 5c4a753fbe5356e11a00db07561d5ddb8c4e2c66 Mon Sep 17 00:00:00 2001
From: Jakob Schiotz <schiotz@fysik.dtu.dk>
Date: Wed, 29 Mar 2023 13:11:46 +0200
Subject: [PATCH 179/601] Bug fix: Tolerance too tight in test suite.

---
 ...22.8.0-Test-too-strict-for-EasyBuild.patch | 53 +++++++++++++++++++
 .../g/GPAW/GPAW-22.8.0-foss-2022a.eb          | 11 ++--
 .../g/GPAW/GPAW-22.8.0-intel-2022a.eb         | 11 ++--
 3 files changed, 67 insertions(+), 8 deletions(-)
 create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch

diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch
new file mode 100644
index 00000000000..f52f396627a
--- /dev/null
+++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch
@@ -0,0 +1,53 @@
+From 79eb7a47726f7e0f644d0b9bddf3840b227a2f73 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Jens=20J=C3=B8rgen=20Mortensen?= <jensj@fysik.dtu.dk>
+Date: Wed, 21 Sep 2022 12:10:16 +0200
+Subject: [PATCH] Test too strict for EasyBuild intel/2020b toolchain
+
+---
+ gpaw/test/gllb/test_variants.py | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/gpaw/test/gllb/test_variants.py b/gpaw/test/gllb/test_variants.py
+index 0b9ede0..8a51261 100644
+--- a/gpaw/test/gllb/test_variants.py
++++ b/gpaw/test/gllb/test_variants.py
+@@ -1,8 +1,8 @@
+-import pytest
+ import numpy as np
++import pytest
+ from ase.build import bulk
+-from gpaw.test import gen
+ from gpaw import GPAW
++from gpaw.test import gen
+ 
+ 
+ def run(xc):
+@@ -19,7 +19,7 @@ def run(xc):
+                 xc=xc,
+                 convergence={'density': 1e-5},
+                 kpts={'size': (1, 1, 1), 'gamma': True},
+-                txt='{}.out'.format(xc))
++                txt=f'{xc}.out')
+     atoms.calc = calc
+     atoms.get_potential_energy()
+     eig_n = calc.get_eigenvalues(kpt=0)
+@@ -35,7 +35,7 @@ def test_wrappers(xc, in_tmp_dir, add_cwd_to_setup_paths):
+     # Check values against regular xc
+     ref_eig_n = run({'GLLBLDA': 'LDA', 'GLLBPBE': 'PBE'}[xc])
+     assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=1e-8), \
+-        "{} error = {}".format(xc, np.max(np.abs(eig_n - ref_eig_n)))
++        f'{xc} error = {np.max(np.abs(eig_n - ref_eig_n))}'
+ 
+ 
+ refs = {'GLLB':
+@@ -70,5 +70,5 @@ refs = {'GLLB':
+ def test_eigenvalues(xc, in_tmp_dir, add_cwd_to_setup_paths):
+     eig_n = run(xc)
+     ref_eig_n = refs[xc]
+-    assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=5e-6), \
+-        "{} error = {}".format(xc, np.max(np.abs(eig_n - ref_eig_n)))
++    assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=2e-5), \
++        f'{xc} error = {np.max(np.abs(eig_n - ref_eig_n))}'
+-- 
+1.8.3.1
+
diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb
index a5bf81c6abc..2a7e04552e6 100644
--- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb
@@ -16,12 +16,15 @@ sources = [SOURCELOWER_TAR_GZ]
 patches = [
     ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1),
     ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0),
+    ('GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch', 1),
 ]
 checksums = [
-    '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c',  # gpaw-22.8.0.tar.gz
-    # GPAW-20.1.0-Add-Easybuild-configuration-files.patch
-    '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15',
-    '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e',  # GPAW-22.8.0-Remove-MPI-compiler-hack.patch
+    {'gpaw-22.8.0.tar.gz': '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c'},
+    {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch':
+     '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'},
+    {'GPAW-22.8.0-Remove-MPI-compiler-hack.patch': '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e'},
+    {'GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch':
+     '207d98ab3b390330f832a77edf5e436b9ec46610add6c0487acaa63b2aa489a1'},
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb
index 126147e70d5..8055d042a4c 100644
--- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb
+++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb
@@ -16,12 +16,15 @@ sources = [SOURCELOWER_TAR_GZ]
 patches = [
     ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1),
     ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0),
+    ('GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch', 1),
 ]
 checksums = [
-    '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c',  # gpaw-22.8.0.tar.gz
-    # GPAW-20.1.0-Add-Easybuild-configuration-files.patch
-    '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15',
-    '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e',  # GPAW-22.8.0-Remove-MPI-compiler-hack.patch
+    {'gpaw-22.8.0.tar.gz': '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c'},
+    {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch':
+     '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'},
+    {'GPAW-22.8.0-Remove-MPI-compiler-hack.patch': '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e'},
+    {'GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch':
+     '207d98ab3b390330f832a77edf5e436b9ec46610add6c0487acaa63b2aa489a1'},
 ]
 
 dependencies = [

From 5e6ec04391cae6a4c8d1ba0d55f0859a2f77df51 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 29 Mar 2023 13:35:10 +0200
Subject: [PATCH 180/601] CuPy: Add some clarifying comments about cuSPARSELt
 and the TestProduct test case.

---
 .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb    | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
index d194347e4cd..ddafffc0fed 100644
--- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
@@ -20,6 +20,7 @@ dependencies = [
     ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM),
     ('NCCL', '2.10.3', versionsuffix),
     ('cuTENSOR', '1.6.1.5', versionsuffix, SYSTEM),
+    # Adding cuSPARSELt currently makes the build fail. Keeping it around for later versions to pick up.
     # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM),
 ]
 
@@ -37,6 +38,7 @@ _skip_tests = [
     'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_',
     'tests/cupy_tests/fft_tests/test_fft.py',
     # float16 has too low precision for these tests as they are written
+    # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details.
     'tests/cupy_tests/linalg_tests/test_product.py::TestProduct',
 ]
 _ignore_list = ' --ignore='.join(_skip_tests)

From d8c727eb366fffecd402d6fe707d470b24c89fd8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Mar 2023 14:42:09 +0200
Subject: [PATCH 181/601] move sources/checksums right below toolchain in
 pyparsing 3.0.9 easyconfig

---
 .../p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb           | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb
index 0c8b7ea8098..5accb085ce1 100644
--- a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb
@@ -11,6 +11,9 @@ client code uses to construct the grammar directly in Python code."""
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
+sources = [SOURCE_TAR_GZ]
+checksums = ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb']
+
 builddependencies = [
     ('binutils', '2.38'),
     ('pkg-config', '0.29.2'),
@@ -24,7 +27,4 @@ download_dep_fail = True
 use_pip = True
 sanity_pip_check = True
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb']
-
 moduleclass = 'data'

From d9c502a888072cc61b3b729b22583ff23b667013 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 29 Mar 2023 16:13:23 +0200
Subject: [PATCH 182/601] Workaround cargo limitations, add missing vendored
 sources

---
 .../b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
index 987340268d8..2daaefe9ffe 100644
--- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
@@ -164,9 +164,20 @@ crates = [
     ('libc', '0.2.103'),
     ('rand_core', '0.6.3'),
     ('remove_dir_all', '0.5.3'),
+    ('redox_syscall', '0.2.10'),
+    ('winapi', '0.3.9'),
+    ('vcpkg', '0.2.15'),
+    ('curl-sys', '0.4.49+curl-7.79.1'),
+    ('openssl-sys', '0.9.67'),
+    ('rand_hc', '0.3.1'),
+    ('bitflags', '1.3.2'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('openssl-src', '111.16.0+1.1.1l'),
+    ('wasi', '0.10.2+wasi-snapshot-preview1'),
 ]
 source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags']
-sources = ['v%(version)s.tar.gz']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
 checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed']
 
 builddependencies = [

From ca8f7152a3141420772568480f277f2262f424f9 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 29 Mar 2023 17:47:12 +0100
Subject: [PATCH 183/601] Pandas removed

---
 easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
index 686bc673215..d6860c0a27e 100644
--- a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb
@@ -27,7 +27,6 @@ dependencies = [
     ('SciPy-bundle', '2022.05'),
     ('scikit-learn', '1.1.2'),
     ('plotly.py', '5.12.0'),
-    ('pandas', '1.5.3'),
     ('matplotlib', '3.5.2'),
     ('HDBSCAN', '0.8.29'),
     ('h5py', '3.7.0'),

From d9f9f658d0670c01d0add1d88e94a9f8e40d9192 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 29 Mar 2023 18:48:26 +0200
Subject: [PATCH 184/601] adding easyconfigs:
 Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb

---
 ...s-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb

diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb
new file mode 100644
index 00000000000..f8e15be6954
--- /dev/null
+++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'Keras'
+version = '2.4.3'
+local_tf_version = '2.5.0'
+versionsuffix = '-TensorFlow-2.5.0'
+
+homepage = 'https://keras.io/'
+description = """
+Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow.
+"""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('Theano', '1.1.2', '-PyMC'),
+    ('PyYAML', '5.3.1'),
+    ('TensorFlow', local_tf_version),  # provides h5py 2.1.0
+]
+
+use_pip = True
+
+exts_list = [
+    ('Keras_Applications', '1.0.8', {
+        'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'],
+    }),
+    ('Keras_Preprocessing', '1.1.2', {
+        'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'],
+    }),
+    (name, version, {
+        'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'math'

From e78d64eabdb621f2d0c3997a90f98669709cd10e Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Thu, 30 Mar 2023 13:08:26 +0200
Subject: [PATCH 185/601] adding easyconfigs: CASTEP-22.11-foss-2022a.eb

---
 .../c/CASTEP/CASTEP-22.11-foss-2022a.eb       | 46 +++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb
new file mode 100644
index 00000000000..b0b068be51f
--- /dev/null
+++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb
@@ -0,0 +1,46 @@
+easyblock = 'ConfigureMake'
+
+name = 'CASTEP'
+version = '22.11'
+
+homepage = 'http://www.castep.org'
+description = """
+CASTEP is an electronic structure materials modelling code based on density
+functional theory (DFT), with functionality including geometry optimization
+molecular dynamics, phonons, NMR chemical shifts and much more.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# CASTEP is proprietary software, available under a free-of-charge license for academic use only.
+# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license.
+sources = [SOURCE_TAR_GZ]
+checksums = ['aca3fc2207c677561293585a4edaf233676a759c5beb8389cf938411226ef1f5']
+
+# Python+numpy are needed for the elastic constants and castepconv utilities, but
+# should work with any system or eb Python including 2.7.
+dependencies = [
+    ('Perl', '5.34.1'),
+]
+
+skipsteps = ['configure']
+
+buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR'
+buildopts += ' castep tools utilities'
+
+preinstallopts = 'mkdir -p %(installdir)s/bin &&'
+installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" INSTALL_DIR="%(installdir)s/bin"'
+installopts += ' install-castep install-tools install-utilities'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl',
+                                     'elastics.py', 'ceteprouts.pm']],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    'castep.mpi --help',
+    'optados.mpi --help',
+]
+
+moduleclass = 'phys'

From bcaca7de6e21e836e392424f2661922404e69ccc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 30 Mar 2023 14:06:34 +0200
Subject: [PATCH 186/601] adding easyconfigs: synthcity-0.2.4-foss-2022a.eb

---
 .../s/synthcity/synthcity-0.2.4-foss-2022a.eb | 165 ++++++++++++++++++
 1 file changed, 165 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb
new file mode 100644
index 00000000000..105a197046b
--- /dev/null
+++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb
@@ -0,0 +1,165 @@
+easyblock = 'PythonBundle'
+
+name = 'synthcity'
+version = '0.2.4'
+
+homepage = 'https://github.com/vanderschaarlab/synthcity'
+description = """A library for generating and evaluating synthetic tabular data."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('lifelines', '0.27.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('pydantic', '1.10.4'),
+    ('Redis', '7.0.8'),
+    ('scikit-learn', '1.1.2'),
+    ('SHAP', '0.41.0'),
+    ('PyTorch', '1.12.0'),
+    ('XGBoost', '1.7.2'),
+    ('tqdm', '4.64.0'),
+    ('Mako', '1.2.0'),
+    ('PyYAML', '6.0'),
+    ('fastai', '2.7.10'),
+    ('h5py', '3.7.0'),
+    ('networkx', '2.8.4'),
+    ('protobuf', '3.19.4'),
+    ('Arrow', '8.0.0'),
+    ('pybind11', '2.9.2'),
+    ('PyTorch-Lightning', '1.8.4'),
+    ('spaCy', '3.4.4'),
+    ('tensorboard', '2.10.0'),
+    ('torchvision', '0.13.1'),
+    ('Brotli-python', '1.0.9'),
+    ('statsmodels', '0.13.1'),
+    ('imbalanced-learn', '0.10.1'),
+    ('Greenlet', '2.0.2'),
+    ('Optuna', '3.1.0'),
+    ('Cython', '0.29.33'),
+    ('cython-blis', '0.9.1'),
+    ('torchtext', '0.14.1'),
+    ('IPython', '8.5.0'),
+]
+
+sanity_pip_check = True
+use_pip = True
+
+exts_list = [
+    ('decaf_synthetic_data', '0.1.6', {
+        'modulename': 'decaf',
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['dc51502f9f72b3fbdbef697238d72ae6b8457f76efc9763a747970ba543d4e0f'],
+    }),
+    ('feather-format', '0.4.1', {
+        'modulename': 'feather',
+        'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'],
+    }),
+    ('fflows', '0.0.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'],
+    }),
+    ('functorch', '0.2.0', {
+        'source_urls': ['https://github.com/pytorch/%(name)s/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['ea6446b60d5e0847140e1a0dcb91d8a7de2b5844bba7c3f7560eb5020a05881f'],
+    }),
+    ('geomloss', '0.2.5', {
+        'checksums': ['dcd851cc3c9625f384d4c18d235a790821162c34a2be503a61966b355b98456e'],
+    }),
+    ('inflate64', '0.3.1', {
+        'checksums': ['b52dd8fefd2ba179e5dfa18d6eca7e2fc822584616271c039d5ef1f9ca90c71c'],
+    }),
+    ('keopscore', '2.1.1', {
+        'checksums': ['07b4d254a28a9d4a43153663856677263dd7112912efacbad83c2a76ea0836f0'],
+    }),
+    ('loguru', '0.6.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['4e2414d534a2ab57573365b3e6d0234dfb1d84b68b7f3b948e6fb743860a77c3'],
+    }),
+    ('monai', '1.1.0', {
+        'source_urls': ['https://github.com/Project-MONAI/MONAI/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['7e4129b4b9b64137f45b59667a80faac0576e4e3af48023e0aef95317f36eab9'],
+    }),
+    ('multivolumefile', '0.2.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'],
+    }),
+    ('nflows', '0.14', {
+        'checksums': ['6299844a62f9999fcdf2d95cb2d01c091a50136bd17826e303aba646b2d11b55'],
+    }),
+    ('opacus', '1.3.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['ef5d6f2aab56901d714ee56fd177a3627d14d820b2ec49cb8bc8a6f52c326507'],
+    }),
+    ('opt_einsum', '3.3.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['2455e59e3947d3c275477df7f5205b30635e266fe6dc300e3d9f9646bfcea147'],
+    }),
+    ('pgmpy', '0.1.21', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['3c442320e7822892813b4eb56e048729d3bde053a707b5bb032685af6b372246'],
+    }),
+    ('py7zr', '0.20.4', {
+        'checksums': ['1d01f98ea1e1f5c49940358691b2076f9a5848056426541e783de33834f59e21'],
+    }),
+    ('pybcj', '1.0.1', {
+        'modulename': 'bcj',
+        'checksums': ['8b682ed08caabfb7c042d4be083e28ddc692afb1deff5567111f8855071b75c3'],
+    }),
+    ('pycox', '0.2.3', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['9ea3c64a4a650ccf6c96cf512712de330f2d75de32122d86995c7cd37ff105d1'],
+    }),
+    ('pycryptodomex', '3.17', {
+        'modulename': 'Crypto',
+        'checksums': ['0af93aad8d62e810247beedef0261c148790c52f3cd33643791cc6396dd217c1'],
+    }),
+    ('pykeops', '2.1.1', {
+        'checksums': ['1931823c746345ce5a5805adad6baa1add772c6fe1800375f7f9a3ddb38b6f71'],
+    }),
+    ('pyppmd', '1.0.0', {
+        'checksums': ['075c9bd297e3b0a87dd7aeabca7fee668218acbe69ecc1c6511064558de8840f'],
+    }),
+    ('pyts', '0.12.0', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['acd66b0cf1fd17d9ce6449335f5da30701f65fdee185d4b918726b62ca6af79d'],
+    }),
+    ('pyzstd', '0.15.4', {
+        'checksums': ['de07ac54f57642f186732075cdce2be3d4a30228c3b17a6d8c6053765dc6eec8'],
+    }),
+    ('texttable', '1.6.7', {
+        'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['b7b68139aa8a6339d2c320ca8b1dc42d13a7831a346b446cb9eb385f0c76310c'],
+    }),
+    ('thinc', '8.1.9', {
+        'checksums': ['8a1e65529c6d0796271d2a7e5ca6ea013fcb7dad69ec609d5093a25808107f51'],
+        # we are using blis 0.9.1
+        # thinc has problems with blis>0.8.0 on Windows only (https://github.com/explosion/thinc/pull/772)
+        'preinstallopts': 'sed -i "s/blis>=0.7.8,<0.8.0/blis>=0.7.8/g" setup.cfg && ',
+    }),
+    ('torchtuples', '0.2.2', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['186625230a149cc09f64116d51b203ffefe78160f5a0445adad195893663f55b'],
+    }),
+    ('tsai', '0.3.5', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['f5b888f7b968d1826a74eab3b8fa9559c6985d8532c017a4d85809e6c8e6cadd'],
+    }),
+    ('xgbse', '0.2.3', {
+        'source_urls': ['https://github.com/loft-br/xgboost-survival-embeddings/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['424448d420331743458bf63558a06a5fbefbad19392718cd0a755d4a4878476c'],
+    }),
+]
+
+sanity_check_commands = [
+    "python -c 'from synthcity.plugins import Plugins'",
+]
+
+moduleclass = 'lib'

From a9b93e699dac74a35b73ccfec697db0b67979737 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 30 Mar 2023 16:50:23 +0200
Subject: [PATCH 187/601] adding easyconfigs: Shapely-2.0.1-foss-2022b.eb

---
 .../s/Shapely/Shapely-2.0.1-foss-2022b.eb     | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb
new file mode 100644
index 00000000000..ab2fa48ba51
--- /dev/null
+++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb
@@ -0,0 +1,27 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Updated: Denis Kristak
+easyblock = 'PythonPackage'
+
+name = 'Shapely'
+version = '2.0.1'
+
+homepage = 'https://github.com/Toblerity/Shapely'
+description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects.
+It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['66a6b1a3e72ece97fc85536a281476f9b7794de2e646ca8a4517e2e3c1446893']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('GEOS', '3.11.1'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'

From 02506a99953aa5de650be4ae3e45d200fcf84e83 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Thu, 30 Mar 2023 17:21:48 +0200
Subject: [PATCH 188/601] dep fixes

---
 .../s/synthcity/synthcity-0.2.4-foss-2022a.eb    | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb
index 105a197046b..2d2a1ab0f5d 100644
--- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb
@@ -3,6 +3,8 @@ easyblock = 'PythonBundle'
 name = 'synthcity'
 version = '0.2.4'
 
+local_pytorch_version = '1.12.0'
+
 homepage = 'https://github.com/vanderschaarlab/synthcity'
 description = """A library for generating and evaluating synthetic tabular data."""
 
@@ -16,7 +18,7 @@ dependencies = [
     ('Redis', '7.0.8'),
     ('scikit-learn', '1.1.2'),
     ('SHAP', '0.41.0'),
-    ('PyTorch', '1.12.0'),
+    ('PyTorch', local_pytorch_version),
     ('XGBoost', '1.7.2'),
     ('tqdm', '4.64.0'),
     ('Mako', '1.2.0'),
@@ -38,8 +40,9 @@ dependencies = [
     ('Optuna', '3.1.0'),
     ('Cython', '0.29.33'),
     ('cython-blis', '0.9.1'),
-    ('torchtext', '0.14.1'),
+    ('torchtext', '0.14.1', '-PyTorch-%s' % local_pytorch_version),
     ('IPython', '8.5.0'),
+    ('MONAI', '1.0.1'),
 ]
 
 sanity_pip_check = True
@@ -59,6 +62,10 @@ exts_list = [
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
         'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'],
     }),
+    ('fsspec', '2022.7.1', {
+        'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
+        'checksums': ['36c5a8e7c4fc20cf32ef6934ac0a122accc8a593ddc8478d30c3ca4dbbd95500'],
+    }),
     ('functorch', '0.2.0', {
         'source_urls': ['https://github.com/pytorch/%(name)s/archive/'],
         'sources': ['v%(version)s.tar.gz'],
@@ -77,11 +84,6 @@ exts_list = [
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
         'checksums': ['4e2414d534a2ab57573365b3e6d0234dfb1d84b68b7f3b948e6fb743860a77c3'],
     }),
-    ('monai', '1.1.0', {
-        'source_urls': ['https://github.com/Project-MONAI/MONAI/archive/'],
-        'sources': ['%(version)s.tar.gz'],
-        'checksums': ['7e4129b4b9b64137f45b59667a80faac0576e4e3af48023e0aef95317f36eab9'],
-    }),
     ('multivolumefile', '0.2.3', {
         'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl',
         'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'],

From 061645335841ac733a5f7e1555b7bff5cc94fe2d Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Thu, 30 Mar 2023 17:49:01 +0200
Subject: [PATCH 189/601] use download_instructions

---
 easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb
index b0b068be51f..8e3491edd65 100644
--- a/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb
@@ -12,8 +12,9 @@ molecular dynamics, phonons, NMR chemical shifts and much more.
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
-# CASTEP is proprietary software, available under a free-of-charge license for academic use only.
-# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license.
+download_instructions = """CASTEP is proprietary software, available under a free-of-charge license for academic use
+only. Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license."""
+
 sources = [SOURCE_TAR_GZ]
 checksums = ['aca3fc2207c677561293585a4edaf233676a759c5beb8389cf938411226ef1f5']
 

From 7e21a9cde3514acd5986acf9e5dd6cc34991b7c7 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Thu, 30 Mar 2023 17:54:47 +0200
Subject: [PATCH 190/601] adding easyconfigs:
 SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb, PETSc-3.18.4-intel-2021b.eb,
 SLEPc-3.18.2-intel-2021b.eb

---
 .../p/PETSc/PETSc-3.18.4-intel-2021b.eb       | 43 +++++++++++++++++++
 .../s/SLEPc/SLEPc-3.18.2-intel-2021b.eb       | 20 +++++++++
 ...iteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb | 31 +++++++++++++
 3 files changed, 94 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
 create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb
 create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
new file mode 100644
index 00000000000..d42525d3bec
--- /dev/null
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
@@ -0,0 +1,43 @@
+name = 'PETSc'
+version = '3.18.4'
+
+homepage = 'https://www.mcs.anl.gov/petsc'
+description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
+ scalable (parallel) solution of scientific applications modeled by partial differential equations."""
+
+toolchain = {'name': 'intel', 'version': '2021b'}
+toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}
+
+source_urls = [
+    'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+    'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'PETSc_ranlib-fix.patch',
+]
+
+builddependencies = [('CMake', '3.22.1')]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),
+    ('Boost', '1.77.0'),
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '6.1.2'),
+    ('MUMPS', '5.4.1', '-metis'),
+    ('SuiteSparse', '5.8.1', '-METIS-5.1.0'),
+    ('Hypre', '2.24.0'),
+]
+
+# enabling --with-mpi4py seems to be totally broken, leads to make errors like:
+# No rule to make target 'mpi4py-build'
+configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 '
+
+shared_libs = 1
+
+# only required when building PETSc in a SLURM job environment
+# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 '
+# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && "
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb
new file mode 100644
index 00000000000..b901d4273a3
--- /dev/null
+++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb
@@ -0,0 +1,20 @@
+name = 'SLEPc'
+version = '3.18.2'
+
+homepage = 'https://www.grycap.upv.es/slepc/'
+description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution
+ of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for
+ either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a
+ partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems."""
+
+toolchain = {'name': 'intel', 'version': '2021b'}
+toolchainopts = {'usempi': True, 'openmp': True}
+
+source_urls = ['https://slepc.upv.es/download/distrib']
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('PETSc', '3.18.4')]
+
+petsc_arch = 'installed-arch-linux2-c-opt'
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb
new file mode 100644
index 00000000000..77da446bc74
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb
@@ -0,0 +1,31 @@
+name = 'SuiteSparse'
+version = '5.8.1'
+local_metis_ver = '5.1.0'
+versionsuffix = '-METIS-%s' % local_metis_ver
+
+homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries manipulate sparse matrices."""
+
+toolchain = {'name': 'intel', 'version': '2021b'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
+sources = ['v%(version)s.tar.gz']
+
+
+builddependencies = [
+    ('CMake', '3.21.1'),
+    ('M4', '1.4.19'),
+]
+
+dependencies = [
+    ('METIS', local_metis_ver),
+    ('MPFR', '4.1.0'),
+]
+
+# make sure that bin/demo can find libsuitesparseconfig.so.5 during build
+prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
+# remove broken symlink
+# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && "
+
+moduleclass = 'numlib'

From f848d4f8ab1a311a47dd52e0628aeee50b89cebe Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Thu, 30 Mar 2023 17:59:28 +0200
Subject: [PATCH 191/601] Added checksums

---
 easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb     | 4 ++++
 easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb     | 1 +
 .../SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb  | 2 +-
 3 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
index d42525d3bec..c98e36180d7 100644
--- a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
@@ -16,6 +16,10 @@ sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'PETSc_ranlib-fix.patch',
 ]
+checksums = [
+    {'petsc-3.18.4.tar.gz': '6173d30637261c5b740c0bea14747759200ca2012c7343139f9216bc296a6394'},
+    {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'},
+]
 
 builddependencies = [('CMake', '3.22.1')]
 
diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb
index b901d4273a3..1db8a8efa48 100644
--- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb
+++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb
@@ -12,6 +12,7 @@ toolchainopts = {'usempi': True, 'openmp': True}
 
 source_urls = ['https://slepc.upv.es/download/distrib']
 sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5bd90a755934e702ab1fdb3320b9fe75ab5fc28c93d364248ea86a372fbe6a62']
 
 dependencies = [('PETSc', '3.18.4')]
 
diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb
index 77da446bc74..d0ac5441697 100644
--- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb
@@ -11,7 +11,7 @@ toolchainopts = {'unroll': True, 'pic': True}
 
 source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
 sources = ['v%(version)s.tar.gz']
-
+checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40']
 
 builddependencies = [
     ('CMake', '3.21.1'),

From 92e0a53623de7b15fbd5d15ec0c32df3fa0baa8d Mon Sep 17 00:00:00 2001
From: Joachim Hein <joachim.hein@math.lu.se>
Date: Thu, 30 Mar 2023 18:18:03 +0200
Subject: [PATCH 192/601] Create Python-bundle-3.10.4-foss-2022a.eb

---
 .../Python-bundle-3.10.4-foss-2022a.eb        | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
new file mode 100644
index 00000000000..5b48c384f20
--- /dev/null
+++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
@@ -0,0 +1,19 @@
+easyblock = 'Bundle'
+
+name = 'Python-bundle'
+version = '3.10.4'
+
+homepage = 'https://easybuild.io/'
+description = """Python distribution with a number of widely used extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """
+
+local_gccver = '11.3.0'
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+dependencies = [
+    ('Python', version),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+    ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)),
+]
\ No newline at end of file

From 203a2789fa04065ffb405094fc3bbe6ebaa67ba2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Thu, 30 Mar 2023 18:53:23 +0200
Subject: [PATCH 193/601] adding easyconfigs: rioxarray-0.14.0-foss-2022a.eb

---
 .../rioxarray/rioxarray-0.14.0-foss-2022a.eb  | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb
new file mode 100644
index 00000000000..57c9a4816f3
--- /dev/null
+++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'rioxarray'
+version = '0.14.0'
+
+homepage = 'https://github.com/corteva/rioxarray'
+description = "geospatial xarray extension powered by rasterio"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('rasterio', '1.3.4'),
+    ('pyproj', '3.4.0'),
+    ('xarray', '2022.6.0'),
+]
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['bbbda47fd7eb04c0986df553f11aa0bdbc9846e75601b8ebd704fc8573bfb835']
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'geo'

From d9bbf999acc97d099ff622455e7a341fac50a59f Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 30 Mar 2023 19:37:13 +0100
Subject: [PATCH 194/601] Add alternative checksum for MONAI 1.0.1

---
 .../easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb  | 3 ++-
 easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb        | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb
index c4ae75df709..134fe42c205 100644
--- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb
@@ -32,7 +32,8 @@ exts_list = [
         'preinstallopts': 'BUILD_MONAI=1',
         'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
-        'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'],
+        'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b',
+                       'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')],
     }),
 ]
 
diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb
index 0314fc871d4..04560e4c6fd 100644
--- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb
@@ -30,7 +30,8 @@ exts_list = [
         'preinstallopts': 'BUILD_MONAI=1',
         'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
-        'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'],
+        'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b',
+                       'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')],
     }),
 ]
 

From 798e5ffeb458399c633cddcbcb13d87cb9c0c36d Mon Sep 17 00:00:00 2001
From: Joachim Hein <joachim.hein@math.lu.se>
Date: Thu, 30 Mar 2023 21:01:21 +0200
Subject: [PATCH 195/601] Updated Python-bundle-3.10.4-foss-2022a.eb for style
 check

---
 .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb       | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
index 5b48c384f20..5df3fd8caf7 100644
--- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
@@ -4,7 +4,8 @@ name = 'Python-bundle'
 version = '3.10.4'
 
 homepage = 'https://easybuild.io/'
-description = """Python distribution with a number of widely used extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """
+description = """Python distribution with a number of widely used 
+extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """
 
 local_gccver = '11.3.0'
 
@@ -16,4 +17,4 @@ dependencies = [
     ('SciPy-bundle', '2022.05'),
     ('matplotlib', '3.5.2'),
     ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)),
-]
\ No newline at end of file
+]

From c355ed5ca0c85585582054834a05fa8c1347eda4 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Thu, 30 Mar 2023 21:50:57 +0200
Subject: [PATCH 196/601] Changed version of SuiteSparse

---
 .../p/PETSc/PETSc-3.18.4-intel-2021b.eb       |  2 +-
 ...teSparse-5.10.1-intel-2021b-METIS-5.1.0.eb | 31 +++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb

diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
index c98e36180d7..37ddfc1c7fc 100644
--- a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
+++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb
@@ -30,7 +30,7 @@ dependencies = [
     ('METIS', '5.1.0'),
     ('SCOTCH', '6.1.2'),
     ('MUMPS', '5.4.1', '-metis'),
-    ('SuiteSparse', '5.8.1', '-METIS-5.1.0'),
+    ('SuiteSparse', '5.10.1', '-METIS-5.1.0'),
     ('Hypre', '2.24.0'),
 ]
 
diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
new file mode 100644
index 00000000000..4da9cfeafa6
--- /dev/null
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
@@ -0,0 +1,31 @@
+name = 'SuiteSparse'
+version = '5.10.1'
+local_metis_ver = '5.1.0'
+versionsuffix = '-METIS-%s' % local_metis_ver
+
+homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries manipulate sparse matrices."""
+
+toolchain = {'name': 'intel', 'version': '2021b'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [
+    ('CMake', '3.21.1'),
+    ('M4', '1.4.19'),
+]
+
+dependencies = [
+    ('METIS', local_metis_ver),
+    ('MPFR', '4.1.0'),
+]
+
+parallel = 1
+# make sure that bin/demo can find libsuitesparseconfig.so.5 during build
+prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
+# remove broken symlink
+# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && "
+
+moduleclass = 'numlib'

From 0d4b9463d995f8e29f13a421615ea51004f3cfe9 Mon Sep 17 00:00:00 2001
From: Orient <orient@inuits.eu>
Date: Thu, 30 Mar 2023 21:54:29 +0200
Subject: [PATCH 197/601] Forgot to add new checksum to SuiteSparse

---
 .../s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
index 4da9cfeafa6..1f3df90eb02 100644
--- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
@@ -11,6 +11,7 @@ toolchainopts = {'unroll': True, 'pic': True}
 
 source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
 sources = ['v%(version)s.tar.gz']
+checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee']
 
 builddependencies = [
     ('CMake', '3.21.1'),

From 6a0864d3d84fa3c4134268b0d5ca6581017529db Mon Sep 17 00:00:00 2001
From: Joachim Hein <joachim.hein@math.lu.se>
Date: Fri, 31 Mar 2023 09:32:17 +0200
Subject: [PATCH 198/601] Added a custom sanity check path

---
 .../p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb         | 1 +
 1 file changed, 1 insertion(+)
 create mode 120000 easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb
new file mode 120000
index 00000000000..c2b7af435fc
--- /dev/null
+++ b/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb
@@ -0,0 +1 @@
+joachim@ip34-194.eduroam-employee.wireless.lu.se.475
\ No newline at end of file

From 712008ec065bc85508e24cd9e162932a2a279286 Mon Sep 17 00:00:00 2001
From: Joachim Hein <joachim.hein@math.lu.se>
Date: Fri, 31 Mar 2023 09:41:58 +0200
Subject: [PATCH 199/601] Removed an emacs back-up file that upset the test
 procedures

---
 .../p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb     | 1 -
 .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb       | 5 +++++
 2 files changed, 5 insertions(+), 1 deletion(-)
 delete mode 120000 easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb
deleted file mode 120000
index c2b7af435fc..00000000000
--- a/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb
+++ /dev/null
@@ -1 +0,0 @@
-joachim@ip34-194.eduroam-employee.wireless.lu.se.475
\ No newline at end of file
diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
index 5df3fd8caf7..993738b8cf7 100644
--- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
@@ -18,3 +18,8 @@ dependencies = [
     ('matplotlib', '3.5.2'),
     ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)),
 ]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ["easybuild/"],
+}
\ No newline at end of file

From af822aee34dc6f449df5ecdb99785e8e3a29d697 Mon Sep 17 00:00:00 2001
From: Joachim Hein <joachim.hein@math.lu.se>
Date: Fri, 31 Mar 2023 10:02:06 +0200
Subject: [PATCH 200/601] Fixing failed style check

---
 .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
index 993738b8cf7..8666c0f0dc9 100644
--- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
@@ -22,4 +22,4 @@ dependencies = [
 sanity_check_paths = {
     'files': [],
     'dirs': ["easybuild/"],
-}
\ No newline at end of file
+}

From 0cdcf232dbc438a33323133e7bb365a25377f90a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 31 Mar 2023 10:12:05 +0200
Subject: [PATCH 201/601] fix paths to perl modules in MAKER v3.01.04

---
 easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
index 6a6d50726d5..fc933ad206d 100644
--- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
@@ -29,7 +29,7 @@ dependencies = [
 exts_defaultclass = 'PerlModule'
 exts_filter = ("perldoc -lm %(ext_name)s ", "")
 
-_libdir = 'lib/perl5/site_perl/%(perlver)s/'
+_libdir = 'lib/perl5/site_perl/%(perlver)s'
 
 exts_list = [
     ('Acme::Damn', '0.08', {
@@ -74,9 +74,10 @@ exts_list = [
     }),
     (name, version, {
         'modulename': False,
+        'preinstallopts': "find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir,
         'postinstallcmds': [
             'cp -a ../bin %(installdir)s/',
-            'cp -an blib/lib/* ../lib/* %%(installdir)s/%s' % _libdir,
+            'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, 
         ],
         'source_tmpl': 'Version_%(version)s.tar.gz',
         'source_urls': ['https://github.com/Yandell-Lab/maker/archive/refs/tags/'],

From 287cd7e4b25b861c633f6eef95080d09cd58c24d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 31 Mar 2023 10:25:47 +0200
Subject: [PATCH 202/601] add comment explaining preinstallopts in MAKER
 v3.01.04

---
 easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
index fc933ad206d..d7f56a73111 100644
--- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
@@ -74,7 +74,8 @@ exts_list = [
     }),
     (name, version, {
         'modulename': False,
-        'preinstallopts': "find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir,
+        # fix hardcoded paths to libraries
+        'preinstallopts': r"find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir,
         'postinstallcmds': [
             'cp -a ../bin %(installdir)s/',
             'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, 

From dff744b196992283ec18a7d5851e675cba806b79 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 31 Mar 2023 10:36:19 +0200
Subject: [PATCH 203/601] fix incorrect ids in BRAKER v2.1.6

---
 .../b/BRAKER/BRAKER-2.1.6-foss-2022a.eb       |  8 +++-
 .../BRAKER-2.1.6_fix-incorrect-ids.patch      | 44 +++++++++++++++++++
 2 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch

diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb
index 1e4df1d9635..f6a9bc03101 100644
--- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb
+++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb
@@ -12,7 +12,11 @@ toolchain = {'name': 'foss', 'version': '2022a'}
 
 source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/']
 sources = ['v%(version)s.tar.gz']
-checksums = ['eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06']
+patches = ['BRAKER-%(version)s_fix-incorrect-ids.patch']
+checksums = [
+    {'v2.1.6.tar.gz': 'eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'},
+    {'BRAKER-2.1.6_fix-incorrect-ids.patch': '2b219de070d109637a2660a456a1f9ced48c58197385e3b3924ae90c84b41d41'},
+]
 
 dependencies = [
     ('Perl', '5.34.1'),
@@ -25,6 +29,8 @@ dependencies = [
     ('Exonerate', '2.4.0'),
     ('BLAST+', '2.13.0'),
     ('Biopython', '1.79'),
+    ('DIAMOND', '2.1.0'),
+    ('CDBtools', '0.99'),
 ]
 
 fix_perl_shebang_for = ['scripts/*.pl']
diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch
new file mode 100644
index 00000000000..3c9df7a402d
--- /dev/null
+++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch
@@ -0,0 +1,44 @@
+From f38630c1cad3e11b525f84d517c7949cb4c2d7eb Mon Sep 17 00:00:00 2001
+From: Katharina Hoff <katharina.hoff@gmail.com>
+Date: Mon, 19 Apr 2021 16:34:57 +0200
+Subject: [PATCH] fixing part of the issue
+ https://github.com/Gaius-Augustus/BRAKER/issues/354 where gene and transcript
+ line have incorrect ids
+
+---
+ scripts/merge_transcript_sets.pl | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/scripts/merge_transcript_sets.pl b/scripts/merge_transcript_sets.pl
+index 04f6c3e..5cfd6c0 100755
+--- a/scripts/merge_transcript_sets.pl
++++ b/scripts/merge_transcript_sets.pl
+@@ -83,14 +83,15 @@
+             my $txid;
+             if($line =~ m/transcript_id/){
+                 $line =~ m/transcript_id "([^"]+)";/;
++
+                 $txid = $1;
+                 push(@{$txid_to_elements{$txid}}, $line);
+                 foreach(@store_for_txid){
+-                    push(@{$txid_to_elements{$txid}}, $_)
++                    push(@{$txid_to_elements{$txid}}, $_);
+                 }
+                 @store_for_txid = ();
+             }else{
+-                $line =~ s/\t([\t]+)$/\tfile_${file_counter}_$1/;
++                $line =~ s/\t([^\t]+)$/\tfile_${file_counter}_$1/;
+                 push(@store_for_txid, $line);
+             }
+             # currently, UTR features are ignored
+@@ -111,9 +112,8 @@
+     # always keep the first occuring transcript structure, only add from other gene sets if it has not been in the set, yet
+     # this might discard alternative UTR splicing isoforms at present
+     while (my ($key, $value) = each (%txid_to_struct_local)){
+-        #print "key is $key and value is $value\n";
++        print "key is $key and value is $value\n";
+         if(not(defined($uniq_struct_to_txid{$value}))){
+-            #print "adding transcript\n";
+             $uniq_struct_to_txid{$value} = $key;
+         }
+     }

From 91fd26887ee40d8265f4eee9101d58c292770216 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 31 Mar 2023 10:37:55 +0200
Subject: [PATCH 204/601] adding easyconfigs: CDBtools-0.99-GCC-11.3.0.eb

---
 .../c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb    | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb
new file mode 100644
index 00000000000..d2dca1af47d
--- /dev/null
+++ b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'MakeCp'
+
+name = 'CDBtools'
+version = '0.99'
+
+homepage = 'http://compbio.dfci.harvard.edu/tgi'
+description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta']
+sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c']
+
+buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"'
+
+files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/cdbfasta', 'bin/cdbyank'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "cdbfasta -v",
+    "cdbyank -v",
+]
+
+moduleclass = 'bio'

From 8f9c3c9a06be44b48e8b69f90e723bb146800cf9 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 31 Mar 2023 10:41:58 +0200
Subject: [PATCH 205/601] remove trailing space in MAKER v3.01.04

---
 easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
index d7f56a73111..4b61ca4d1d3 100644
--- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
+++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb
@@ -78,7 +78,7 @@ exts_list = [
         'preinstallopts': r"find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir,
         'postinstallcmds': [
             'cp -a ../bin %(installdir)s/',
-            'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, 
+            'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir,
         ],
         'source_tmpl': 'Version_%(version)s.tar.gz',
         'source_urls': ['https://github.com/Yandell-Lab/maker/archive/refs/tags/'],

From 4f1e6593cc2482dd561e656456838c52d6e2af6a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 1 Apr 2023 09:42:04 +0200
Subject: [PATCH 206/601] adding easyconfigs: LoRDEC-0.9-gompi-2022a.eb,
 GATB-Core-1.4.2-gompi-2022a.eb and patches: LoRDEC-0.9_GATB.patch,
 LoRDEC-0.9_GraphVector.patch, GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch

---
 .../GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb  |  40 +++
 ...-Core-1.4.2_no-thirdparty-boost-hdf5.patch | 232 ++++++++++++++++++
 .../l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb        |  45 ++++
 .../l/LoRDEC/LoRDEC-0.9_GATB.patch            |  13 +
 .../l/LoRDEC/LoRDEC-0.9_GraphVector.patch     |  73 ++++++
 5 files changed, 403 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb
 create mode 100644 easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch
 create mode 100644 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb
 create mode 100644 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch
 create mode 100644 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch

diff --git a/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb
new file mode 100644
index 00000000000..2d4407c3699
--- /dev/null
+++ b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb
@@ -0,0 +1,40 @@
+easyblock = 'CMakeMake'
+
+name = 'GATB-Core'
+version = '1.4.2'
+
+homepage = 'https://gatb.inria.fr/software/gatb-core'
+description = """GATB-Core is a high-performance and low memory footprint C++ library that provides a set of highly
+ efficient algorithms to analyse NGS data sets"""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://github.com/GATB/gatb-core/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch']
+checksums = [
+    {'v1.4.2.tar.gz': '824c84a3712973746b977a9d49923fd499021a894225231100eaad1a66e9742d'},
+    {'GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch':
+     '938ff686e1fc8170b8ef4a73c1c0af059eb3eb76a6251b44a3dfddf991e05c63'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Doxygen', '1.9.4'),
+]
+
+dependencies = [
+    ('Boost', '1.79.0'),
+    ('HDF5', '1.12.2'),
+]
+
+start_dir = 'gatb-core'
+
+preconfigopts = "rm -r %(start_dir)s/thirdparty/{boost,hdf5} && "
+
+sanity_check_paths = {
+    'files': ['bin/dbginfo', 'bin/leon', 'lib/libgatbcore.a'],
+    'dirs': ['include/gatb'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch
new file mode 100644
index 00000000000..e9e4b86b9c2
--- /dev/null
+++ b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch
@@ -0,0 +1,232 @@
+don't use vendored boost/hdf5 from gatb-core/thirdparty
+author: Kenneth Hoste (HPC-UGent)
+diff -ru gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt gatb-core-1.4.2/gatb-core/CMakeLists.txt
+--- gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/CMakeLists.txt	2023-03-31 21:25:42.862864064 +0200
+@@ -209,7 +209,7 @@
+ set (gatb-core-includes ${PROJECT_BINARY_DIR}/include  ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE} ${PROJECT_SOURCE_DIR}/src  ${PROJECT_SOURCE_DIR}/thirdparty ${gatb-core-extra-libraries-inc})
+ 
+ # We define the libraries used for linking binary based on gatb core
+-set (gatb-core-libraries   gatbcore-static  dl  pthread  z hdf5-static ${gatb-core-extra-libraries})
++set (gatb-core-libraries   gatbcore-static  dl  pthread  z hdf5 ${gatb-core-extra-libraries})
+ 
+ # We define the directory where to find cmake helpers
+ set (gatb-core-cmake  ${CMAKE_MODULE_PATH})
+@@ -252,12 +252,6 @@
+ ADD_SUBDIRECTORY(thirdparty)
+ 
+ ################################################################################
+-#  DEPENDENCIES 
+-################################################################################
+-# we must be sure that hdf5 is built and installed before building gatb-core
+-ADD_DEPENDENCIES (gatbcore-static hdf5-static hdf5_postbuild)
+-
+-################################################################################
+ #  DOCUMENTATION GENERATION 
+ ################################################################################
+ IF (EXISTS "${PROJECT_SOURCE_DIR}/doc")
+@@ -286,7 +280,6 @@
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt  DESTINATION . OPTIONAL)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE              DESTINATION . OPTIONAL)
+     INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md      DESTINATION . OPTIONAL)
+-    INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
+ ENDIF()
+ 
+ ################################################################################
+--- gatb-core-1.4.2.orig/gatb-core/thirdparty/CMakeLists.txt	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/thirdparty/CMakeLists.txt	2023-03-31 14:39:11.999034862 +0200
+@@ -1,54 +1,3 @@
+-################################################################################
+-#  HDF5 GENERATION 
+-################################################################################
+-
+-#SET (HDF5_ENABLE_THREADSAFE       ON)
+-#SET (H5_HAVE_THREADSAFE 1)
+-
+-##########  MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED  ##########
+-SET (HDF5_BUILD_TOOLS             ON CACHE BOOL "Build HDF5 Tools")
+-#SET (CMAKE_EXE_LINKER_FLAGS       "-lpthread -lz")
+-
+-SET (HDF5_EXTERNALLY_CONFIGURED     ON)
+-
+-#SET (HDF5_INSTALL_BIN_DIR           ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
+-#SET (HDF5_INSTALL_LIB_DIR           ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
+-SET (HDF5_INSTALL_BIN_DIR           bin)
+-SET (HDF5_INSTALL_LIB_DIR           lib)
+-
+-SET (HDF5_INSTALL_INCLUDE_DIR       ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
+-SET (HDF5_INSTALL_DATA_DIR          ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+-SET (HDF5_INSTALL_CMAKE_DIR         ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+-
+-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+-    SET (HDF5_EXPORTED_TARGETS          "gatb-hdf5")
+-ENDIF()
+-
+-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB)
+-	OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
+-ENDIF()
+-
+-# We don't want warnings from HDF5 compilation
+-set (COMPILE_DEFINITIONS  "${COMPILE_DEFINITIONS}  -w")
+-add_definitions (${COMPILE_DEFINITIONS})
+-
+-# add HDF5 generation
+-ADD_SUBDIRECTORY (hdf5)
+-
+-# We add a custom target for copying header files.
+-add_custom_target (hdf5_postbuild ALL)
+-
+-# We build the output directory
+-add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
+-
+-# We define all the header files to be copied
+-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
+-
+-# We copy each header file
+-foreach (header ${headerfiles})
+-  add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR}  )
+-endforeach()
+-
+ # include other smaller libraries (json, Boophf)
+ 
+ add_custom_target (thirdparty_copy ALL)
+@@ -63,7 +12,6 @@
+ #  INSTALL 
+ ################################################################################
+ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+-    INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include)
+     INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/json DESTINATION include)
+     INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/BooPHF DESTINATION include)
+ ENDIF ()
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp	2023-03-31 10:40:57.005450131 +0200
+@@ -35,7 +35,7 @@
+ #include <stdint.h>
+ #include <algorithm>
+ #include <iostream>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ #include <gatb/system/api/Exception.hpp>
+ #include <gatb/system/api/config.hpp>
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp	2023-03-31 10:40:57.005450131 +0200
+@@ -33,7 +33,7 @@
+ /********************************************************************************/
+ 
+ #include <iostream>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp	2023-03-31 10:40:57.005450131 +0200
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ extern const unsigned char revcomp_4NT[];
+ extern const unsigned char comp_NT    [];
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp	2023-03-31 10:40:57.006450171 +0200
+@@ -31,7 +31,7 @@
+ /********************************************************************************/
+ 
+ #include <sys/types.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp	2023-03-31 10:40:57.007450212 +0200
+@@ -28,7 +28,7 @@
+ 
+ #include <gatb/system/api/ISmartPointer.hpp>
+ #include <gatb/tools/storage/impl/Storage.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp	2023-03-31 10:40:57.007450212 +0200
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp	2023-03-31 10:40:57.008450252 +0200
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp	2020-04-12 23:15:34.000000000 +0200
++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp	2023-03-31 10:40:57.008450252 +0200
+@@ -33,7 +33,7 @@
+ #include <gatb/tools/storage/impl/CollectionHDF5.hpp>
+ #include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp>
+ #include <gatb/system/impl/System.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ #include <sstream>
+ 
+ /********************************************************************************/
diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb
new file mode 100644
index 00000000000..2d6b08e5a0e
--- /dev/null
+++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb
@@ -0,0 +1,45 @@
+easyblock = 'MakeCp'
+
+name = 'LoRDEC'
+version = '0.9'
+
+homepage = 'https://www.lirmm.fr/~rivals/lordec'
+description = """Program for correcting sequencing errors in long reads (e.g., PacBio, Oxford Nanopore) using highly
+accurate short reads (e.g., Illumina)."""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/']
+sources = ['lordec-src_%(version)s.tar.bz2']
+patches = [
+    'LoRDEC-0.9_GATB.patch',
+    'LoRDEC-0.9_GraphVector.patch',
+]
+checksums = [
+    {'lordec-src_0.9.tar.bz2': '8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b'},
+    {'LoRDEC-0.9_GATB.patch': '8ff5e097455bb6ea515423bc76059f64d1983eb4873e640cd5021f00be85ca99'},
+    {'LoRDEC-0.9_GraphVector.patch': 'f7ccef2e3149ac5017eebbb9536651a5da5ad51d5021c20f16ab1acd6daa9db0'},
+]
+
+local_gatb_version = '1.4.2'
+dependencies = [
+    ('Boost', '1.79.0'),
+    ('GATB-Core', local_gatb_version),
+]
+
+build_cmd_targets = 'lordec_%s' % ''.join(local_gatb_version.split('.'))
+
+buildopts = "AUTOMATIC_LIBBOOST_LOCAL_INSTALL=no GATB=${EBROOTGATBMINCORE}"
+
+local_bins = ['lordec-%s' % x for x in ('build-SR-graph', 'correct', 'stat', 'trim', 'trim-split')]
+
+files_to_copy = [(local_bins, 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%s --help 2>&1 | grep 'using GATB v%s'" % (x, local_gatb_version) for x in local_bins]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch
new file mode 100644
index 00000000000..11304be190c
--- /dev/null
+++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch
@@ -0,0 +1,13 @@
+don't hardcode path to include/gatb/gatb_core.hpp so we can use GATB-Core provided as dependency
+author: Kenneth Hoste (HPC-UGent)
+--- lordec-src_0.9/Makefile.orig	2023-03-31 09:54:40.838204432 +0200
++++ lordec-src_0.9/Makefile	2023-03-31 09:55:42.987061551 +0200
+@@ -63,7 +63,7 @@
+ $(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): boost_include/boost/graph/graph_traits.hpp
+ endif
+ # ANYWAY we need GATB (compiled and installed) to compile all the objects
+-$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): gatb_v$(GATBVERSION)$(SUFFIX)/include/gatb/gatb_core.hpp
++$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): $(GATB)/include/gatb/gatb_core.hpp
+ 
+ # get version from a file
+ VERSION := $(shell cat version.txt)
diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch
new file mode 100644
index 00000000000..1a47343a0df
--- /dev/null
+++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch
@@ -0,0 +1,73 @@
+diff -ru lordec-src_0.9.orig/lordec-correct.h lordec-src_0.9/lordec-correct.h
+--- lordec-src_0.9.orig/lordec-correct.h	2018-06-04 15:44:49.000000000 +0200
++++ lordec-src_0.9/lordec-correct.h	2023-03-31 22:17:39.105922332 +0200
+@@ -160,11 +160,11 @@
+   // store the neighbors of begin node in the stack
+ 
+ #if defined(GATB_V110)
+-  Graph::Vector<Edge> neighbors = graph.successors<Edge>(begin);
++  GraphVector<Edge> neighbors = graph.successors<Edge>(begin);
+ #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141)
+   GraphVector<Edge> neighbors = graph.successorsEdge(begin);
+ #else
+-  Graph::Vector<Edge> neighbors = graph.successorsEdge(begin);
++  GraphVector<Edge> neighbors = graph.successorsEdge(begin);
+ #endif
+ 
+   //  if (neighbors.size() == 1)
+@@ -221,11 +221,11 @@
+         }
+       }
+ #if defined(GATB_V110)
+-      Graph::Vector<Edge> neighbors = graph.successors<Edge>(cnode);
++      GraphVector<Edge> neighbors = graph.successors<Edge>(cnode);
+ #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141)
+       GraphVector<Edge> neighbors = graph.successorsEdge(cnode);
+ #else
+-      Graph::Vector<Edge> neighbors = graph.successorsEdge(cnode);
++      GraphVector<Edge> neighbors = graph.successorsEdge(cnode);
+ #endif
+ 
+       //      if (neighbors.size() == 1)
+@@ -328,11 +328,11 @@
+ 
+   // store the neighbors of begin node in the stack
+ #if defined(GATB_V110)
+-  Graph::Vector<Edge> neighbors = graph.successors<Edge>(begin);
++  GraphVector<Edge> neighbors = graph.successors<Edge>(begin);
+ #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141)
+   GraphVector<Edge> neighbors = graph.successorsEdge(begin);
+ #else
+-  Graph::Vector<Edge> neighbors = graph.successorsEdge(begin);
++  GraphVector<Edge> neighbors = graph.successorsEdge(begin);
+ #endif
+   for (i = neighbors.size()-1; i>= 0; i--) {
+     nodes.push(new stack_element(neighbors[i].to, 1, ascii(neighbors[i].nt)));
+@@ -396,11 +396,11 @@
+       else {
+ 
+ #if defined(GATB_V110)
+-        Graph::Vector<Edge> neighbors = graph.successors<Edge>(cnode);
++        GraphVector<Edge> neighbors = graph.successors<Edge>(cnode);
+ #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141)
+         GraphVector<Edge> neighbors = graph.successorsEdge(cnode);
+ #else
+-        Graph::Vector<Edge> neighbors = graph.successorsEdge(cnode);
++        GraphVector<Edge> neighbors = graph.successorsEdge(cnode);
+ #endif
+         for(i=neighbors.size()-1; i>=0; i--) {
+           Edge e = neighbors[i];
+@@ -450,11 +450,11 @@
+ 
+   while (true) {
+ #if defined(GATB_V110)
+-    Graph::Vector<Edge> neighbors = graph.successors<Edge>(node);
++    GraphVector<Edge> neighbors = graph.successors<Edge>(node);
+ #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141)
+     GraphVector<Edge> neighbors = graph.successorsEdge(node);
+ #else
+-    Graph::Vector<Edge> neighbors = graph.successorsEdge(node);
++    GraphVector<Edge> neighbors = graph.successorsEdge(node);
+ #endif
+     if (neighbors.size() == 0) // dead end
+       return DEADEND;

From 09c877cb4fe47f9fdeda7e7798dbd7a6b8936321 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Sat, 1 Apr 2023 09:09:43 +0100
Subject: [PATCH 207/601] Delete SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb

---
 ...iteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb | 31 -------------------
 1 file changed, 31 deletions(-)
 delete mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb
deleted file mode 100644
index d0ac5441697..00000000000
--- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb
+++ /dev/null
@@ -1,31 +0,0 @@
-name = 'SuiteSparse'
-version = '5.8.1'
-local_metis_ver = '5.1.0'
-versionsuffix = '-METIS-%s' % local_metis_ver
-
-homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
-description = """SuiteSparse is a collection of libraries manipulate sparse matrices."""
-
-toolchain = {'name': 'intel', 'version': '2021b'}
-toolchainopts = {'unroll': True, 'pic': True}
-
-source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
-sources = ['v%(version)s.tar.gz']
-checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40']
-
-builddependencies = [
-    ('CMake', '3.21.1'),
-    ('M4', '1.4.19'),
-]
-
-dependencies = [
-    ('METIS', local_metis_ver),
-    ('MPFR', '4.1.0'),
-]
-
-# make sure that bin/demo can find libsuitesparseconfig.so.5 during build
-prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
-# remove broken symlink
-# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && "
-
-moduleclass = 'numlib'

From c1187aeaefd4da3e50db9adaf0b231468a9e244d Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Sat, 1 Apr 2023 09:10:11 +0100
Subject: [PATCH 208/601] disable optimisation report to reduce memory usage
 during compile

---
 .../SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
index 1f3df90eb02..254c739d1c6 100644
--- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
@@ -26,7 +26,7 @@ dependencies = [
 parallel = 1
 # make sure that bin/demo can find libsuitesparseconfig.so.5 during build
 prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
-# remove broken symlink
-# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && "
+# disable optimisation report to reduce memory use during compile
+prebuildopts += 'sed -i "s/-qopt-report=5/-qopt-report=0/" GraphBLAS/CMakeLists.txt && '
 
 moduleclass = 'numlib'

From 123066044e3ef4e20ddd011bd49386dca425e1c6 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Sat, 1 Apr 2023 09:16:51 +0100
Subject: [PATCH 209/601] no need to restrict parallel build now

---
 .../s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
index 254c739d1c6..ade731aac57 100644
--- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
+++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb
@@ -23,7 +23,6 @@ dependencies = [
     ('MPFR', '4.1.0'),
 ]
 
-parallel = 1
 # make sure that bin/demo can find libsuitesparseconfig.so.5 during build
 prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && "
 # disable optimisation report to reduce memory use during compile

From 57940d1b0f453fffd4d01f0001242a903fe49983 Mon Sep 17 00:00:00 2001
From: anselmicz <jakubkropacek@email.cz>
Date: Sat, 1 Apr 2023 10:26:21 +0200
Subject: [PATCH 210/601] adding easyconfigs: nano-7.2-GCCcore-12.2.0.eb

---
 .../n/nano/nano-7.2-GCCcore-12.2.0.eb         | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..99cb4947e27
--- /dev/null
+++ b/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'nano'
+version = '7.2'
+
+homepage = 'https://www.nano-editor.org/'
+docurls = 'https://www.nano-editor.org/docs.php'
+description = """a simple editor, inspired by Pico"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['b4edaab0a037b5760484907c674e980053896f33759e43f834a212145fd085f1']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [('ncurses', '6.3')]
+
+sanity_check_paths = {
+    'files': ['bin/nano'],
+    'dirs': ['bin', 'share'],
+}
+
+sanity_check_commands = ['nano --version']
+
+moduleclass = 'tools'

From ad9eca9f6af3738fff671eddba8e4bcdfb65e739 Mon Sep 17 00:00:00 2001
From: anselmicz <jakubkropacek@email.cz>
Date: Sat, 1 Apr 2023 10:38:10 +0200
Subject: [PATCH 211/601] adding easyconfigs: fio-3.34-GCCcore-12.2.0.eb

---
 .../f/fio/fio-3.34-GCCcore-12.2.0.eb          | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..0b7184963e5
--- /dev/null
+++ b/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'fio'
+version = '3.34'
+
+homepage = 'https://github.com/axboe/fio'
+docurls = 'https://fio.readthedocs.io/en/latest/index.html'
+description = 'Flexible I/O tester'
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+github_account = 'axboe'
+source_urls = [GITHUB_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['42ea28c78d269c4cc111b7516213f4d4b32986797a710b0ff364232cc7a3a0b7']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/fio'],
+    'dirs': ['bin', 'man', 'share'],
+}
+
+sanity_check_commands = ['fio -h']
+
+moduleclass = 'tools'

From ae27c8ffd2a9c8ccea3b0d7e3ebd9310ec67da34 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 1 Apr 2023 10:09:13 +0100
Subject: [PATCH 212/601] disable mpi/python in Boost
 (intel-compilers/2021.4.0)

---
 .../b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb            | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb
index f0fce1ec0af..efefe29ecc3 100644
--- a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb
+++ b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb
@@ -24,6 +24,8 @@ preconfigopts = "sed -i 's/-static//g' tools/build/src/engine/build.sh && "
 # see also https://github.com/boostorg/build/issues/647
 preconfigopts += "sed -i 's/{TOOLSET}/{B2_TOOLSET}/g' tools/build/src/engine/build.sh && "
 
+configopts = '--without-libraries=python,mpi'
+
 # disable MPI, build Boost libraries with tagged layout
 boost_mpi = False
 tagged_layout = True

From b9f663389c2a00427abc9a8e7e9f46ddea337389 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 1 Apr 2023 11:18:56 +0200
Subject: [PATCH 213/601] add missing description + author to LoRDEC patch

---
 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb    | 2 +-
 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb
index 2d6b08e5a0e..9de77dd4e7b 100644
--- a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb
+++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb
@@ -18,7 +18,7 @@ patches = [
 checksums = [
     {'lordec-src_0.9.tar.bz2': '8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b'},
     {'LoRDEC-0.9_GATB.patch': '8ff5e097455bb6ea515423bc76059f64d1983eb4873e640cd5021f00be85ca99'},
-    {'LoRDEC-0.9_GraphVector.patch': 'f7ccef2e3149ac5017eebbb9536651a5da5ad51d5021c20f16ab1acd6daa9db0'},
+    {'LoRDEC-0.9_GraphVector.patch': '8c42dda643f8e1f79ee7d4ea2e3d8904cb755dc44cb907ada35b1e2873605ae5'},
 ]
 
 local_gatb_version = '1.4.2'
diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch
index 1a47343a0df..da7be67c7df 100644
--- a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch
+++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch
@@ -1,3 +1,5 @@
+port LoRDEC 0.9 to gatb-core >= 1.3.0 by replacing Graph::Vector to GraphVector
+author: Kenneth Hoste (HPC-UGent)
 diff -ru lordec-src_0.9.orig/lordec-correct.h lordec-src_0.9/lordec-correct.h
 --- lordec-src_0.9.orig/lordec-correct.h	2018-06-04 15:44:49.000000000 +0200
 +++ lordec-src_0.9/lordec-correct.h	2023-03-31 22:17:39.105922332 +0200

From e68cd18f683f56f09e2933c96bbb1188805c4e1a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Sat, 1 Apr 2023 11:37:18 +0200
Subject: [PATCH 214/601] adding easyconfigs: SoPlex-2.2.1-GCC-11.3.0.eb,
 ZIMPL-3.3.4-GCCcore-11.3.0.eb, SCIP-3.2.1-GCC-11.3.0.eb,
 GOBNILP-1.6.3-GCC-11.3.0.eb and patches:
 GOBNILP-1.6.3_use-eb-build-env.patch,
 LOP-3.2.1_standalone-scip-lop-build.patch

---
 .../g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb     | 63 +++++++++++++++
 .../GOBNILP-1.6.3_use-eb-build-env.patch      | 79 +++++++++++++++++++
 .../LOP-3.2.1_standalone-scip-lop-build.patch | 41 ++++++++++
 .../s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb           | 58 ++++++++++++++
 .../s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb       | 38 +++++++++
 .../z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb     | 42 ++++++++++
 6 files changed, 321 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch
 create mode 100644 easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch
 create mode 100644 easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb
new file mode 100644
index 00000000000..565232387de
--- /dev/null
+++ b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb
@@ -0,0 +1,63 @@
+easyblock = 'Bundle'
+
+name = 'GOBNILP'
+version = '1.6.3'
+_nodots_version = version.replace('.', '')
+_scip_version = '3.2.1'
+_scip_nodots_version = _scip_version.replace('.', '')
+
+homepage = 'https://www.cs.york.ac.uk/aig/sw/gobnilp/'
+description = """GOBNILP (Globally Optimal Bayesian Network learning using Integer Linear
+Programming) is a C program which learns Bayesian networks from complete
+discrete data or from local scores."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+dependencies = [
+    ('SCIP', _scip_version),
+    ('ZIMPL', '3.3.4'),
+    ('SoPlex', '2.2.1'),
+    ('GMP', '6.2.1'),
+    ('libreadline', '8.1'),
+    ('ncurses', '6.3'),
+    ('zlib', '1.2.12'),
+]
+
+default_easyblock = 'MakeCp'
+
+components = [
+    ('LOP', _scip_version, {
+        'source_urls': ['https://github.com/scipopt/scip/archive/refs/tags/'],
+        'sources': ['v%s.tar.gz' % _scip_nodots_version],
+        'patches': ['LOP-%(version)s_standalone-scip-lop-build.patch'],
+        'checksums': [
+            {'v321.tar.gz':
+                '015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb'},
+            {'LOP-3.2.1_standalone-scip-lop-build.patch':
+                'f996e56f1311fa4a613635b38969da731faf0ea9f10097799b1fa9a84598651e'},
+        ],
+        'start_dir': 'scip-%s/examples/%%(name)s' % _scip_nodots_version,
+        'buildopts': '%(namelower)s COMP=gnu OPT=opt LPS=spx2',
+        'files_to_copy': [(['bin/%(namelower)s'], 'bin')],
+    }),
+    (name, version, {
+        'source_urls': ['http://www.cs.york.ac.uk/aig/sw/gobnilp'],
+        'sources': ['%(namelower)s%(version)s.tar.gz'],
+        'patches': ['%(name)s-%(version)s_use-eb-build-env.patch'],
+        'checksums': [
+            {'gobnilp1.6.3.tar.gz':
+                'b31e5c87032f85f7404654beca47d472fd6c5dd7a5f82108bd5043ff0b8fa33c'},
+            {'GOBNILP-1.6.3_use-eb-build-env.patch':
+                '9235ec8b9d05d9915f9961d4b46c2220e0d3b75f555a226a5667dcc69d76dae9'},
+        ],
+        'start_dir': '%(namelower)s' + _nodots_version,
+        'files_to_copy': [(['bin/%(namelower)s'], 'bin')],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gobnilp', 'bin/lop'],
+    'dirs': [],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch
new file mode 100644
index 00000000000..e730aa76abf
--- /dev/null
+++ b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch
@@ -0,0 +1,79 @@
+Use build environment and dependencies from EasyBuild
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- Makefile.orig	2023-03-31 18:33:07.943785000 +0200
++++ Makefile	2023-03-31 18:42:53.636293000 +0200
+@@ -5,15 +5,25 @@
+ # This file was created by editing the Makefile for the linear ordering
+ # example in SCIP
+ 
+-# Set the path the SCIP directory
+-SCIPDIR = scip
+-
+-# Include default project Makefile from SCIP
+-include $(SCIPDIR)/make/make.project
++# Set paths and flags to SCIP libraries
++SCIPDIR        = $(EBROOTSCIP)
++SCIPLIB        = scip
++OBJSCIPLIB     = objscip
++LPILIB         = lpispx2
++NLPILIB        = nlpi.cppad
++LPSLDFLAGS     = -lzimpl -lsoplex -lgmp -lreadline -lncurses -lz
++
++# Set paths to LOP
++LOPSRC			=	../scip-321/examples/LOP/src
++LOPOBJ			=	../scip-321/examples/LOP/obj/cons_linearordering.o
+ 
+ # This missing for scip < 3
+ VALGRIND = false
+ 
++SRCDIR = src
++OBJDIR = obj
++BINDIR = bin
++
+ # Declare the phony targets
+ .PHONY: all doxygen manual pedmanual gobnilp clean test
+ 
+@@ -46,7 +57,7 @@
+ MAINSRC			=	$(wildcard $(SRCDIR)/*.c)
+ MAINOBJ			=	$(notdir $(MAINSRC:.c=.o))
+ 
+-MAIN				=	$(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION)
++MAIN				=	$(MAINNAME)
+ MAINFILE			=	$(BINDIR)/$(MAIN)
+ ifeq ($(OSTYPE),mingw)
+ 	MAINSHORTLINK	=	$(BINDIR)/$(MAINNAME).exe
+@@ -63,7 +74,7 @@
+ LATEXCMD			=	@pdflatex -halt-on-error -interaction=errorstopmode
+ 
+ #Needs to appear first so that "make" makes gobnilp
+-gobnilp: $(SCIP) $(MAINFILE) $(MAINSHORTLINK)
++gobnilp: $(MAINFILE) $(MAINSHORTLINK)
+ 
+ #-----------------------------------------------------------------------
+ #----------------------------      All      ----------------------------
+@@ -161,19 +172,16 @@
+ 
+ $(MAINSHORTLINK): $(MAINFILE)
+ 		@rm -f $@
+-		@cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@)
+ 
+-$(MAINFILE): $(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES)
+-		@echo "-> linking $@"
+-		@$(LINKCXX) $(STATICFLAG) $(MAINOBJFILES) \
+-		$(LINKCXX_L)$(SCIPDIR)/lib $(LINKCXX_l)$(SCIPLIB)$(LINKLIBSUFFIX) \
+-                $(LINKCXX_l)$(OBJSCIPLIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(LPILIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(NLPILIB)$(LINKLIBSUFFIX) \
+-                $(OFLAGS) $(LPSLDFLAGS) \
+-		$(LDFLAGS) $(LINKCXX_o)$@
++$(MAINFILE): $(BINDIR) $(OBJDIR) $(MAINOBJFILES)
++		echo "-> linking $@"
++		$(CXX) -static $(MAINOBJFILES) $(LOPOBJ) \
++		-L$(SCIPDIR)/lib -l$(SCIPLIB) -l$(OBJSCIPLIB) -l$(LPILIB) -l$(NLPILIB) \
++		$(LDFLAGS) $(LPSLDFLAGS) -o $@
+ 
+ $(OBJDIR)/%.o: $(SRCDIR)/%.c
+ 		@echo "-> compiling $*.c"
+-		@$(CC) $(FLAGS) $(OFLAGS) $(BINOFLAGS) $(CFLAGS) -c -g $< $(CC_o)$@
++		@$(CC) $(CFLAGS) $(CPPFLAGS) -I$(LOPSRC) -c -g $< -o $@
+ 
+ $(OBJDIR):
+ 		@-mkdir -p $(OBJDIR)
diff --git a/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch b/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch
new file mode 100644
index 00000000000..9fbb54ef086
--- /dev/null
+++ b/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch
@@ -0,0 +1,41 @@
+Build LOP example standalone without triggering a full build of SCIP
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- Makefile.orig	2023-03-31 18:52:55.793723000 +0200
++++ Makefile	2023-03-31 18:54:59.590029000 +0200
+@@ -29,6 +29,7 @@
+ #-----------------------------------------------------------------------------
+ 
+ include $(SCIPDIR)/make/make.project
++OBJDIR		=	obj
+ 
+ #-----------------------------------------------------------------------------
+ # Main Program
+@@ -39,9 +40,9 @@
+ MAINSRC		=	$(addprefix $(SRCDIR)/,$(MAINOBJ:.o=.c))
+ MAINDEP		=	$(SRCDIR)/depend.cmain.$(OPT)
+ 
+-MAIN		=	$(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION)
++MAIN		=	$(MAINNAME)
+ MAINFILE	=	$(BINDIR)/$(MAIN)
+-MAINSHORTLINK	=	$(BINDIR)/$(MAINNAME)
++MAINSHORTLINK	=	$(MAINNAME)
+ MAINOBJFILES	=	$(addprefix $(OBJDIR)/,$(MAINOBJ))
+ 
+ #-----------------------------------------------------------------------------
+@@ -79,7 +80,6 @@
+ 
+ $(MAINSHORTLINK):	$(MAINFILE)
+ 		@rm -f $@
+-		cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@)
+ 
+ $(OBJDIR):
+ 		@-mkdir -p $(OBJDIR)
+@@ -123,7 +123,7 @@
+ 
+ 
+ # main target
+-$(MAINFILE):	$(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES)
++$(MAINFILE):	$(BINDIR) $(OBJDIR) $(MAINOBJFILES)
+ 		@echo "-> linking $@"
+ ifeq ($(VERBOSE),true)
+ 		$(LINKCXX) $(MAINOBJFILES) \
diff --git a/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb
new file mode 100644
index 00000000000..ac0cfca19e8
--- /dev/null
+++ b/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb
@@ -0,0 +1,58 @@
+easyblock = 'ConfigureMake'
+
+name = 'SCIP'
+version = '3.2.1'
+
+homepage = 'https://www.scipopt.org/'
+description = """SCIP is currently one of the fastest non-commercial solvers for mixed integer
+programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a
+framework for constraint integer programming and branch-cut-and-price. It
+allows for total control of the solution process and the access of detailed
+information down to the guts of the solver."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'scipopt'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%s.tar.gz' % version.replace('.', '')]
+checksums = ['015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb']
+
+dependencies = [
+    ('SoPlex', '2.2.1'),
+    ('ZIMPL', '3.3.4'),
+    ('GMP', '6.2.1'),
+    ('libreadline', '8.1'),
+    ('zlib', '1.2.12'),
+]
+
+skipsteps = ['configure']
+
+# prepare symlinks to installation files of dependencies
+prebuildopts = 'mkdir -p lib && '
+prebuildopts += 'ln -sf "$EBROOTSOPLEX/include" "lib/spxinc" && '
+prebuildopts += 'ln -sf "$EBROOTZIMPL/include" "lib/zimplinc" && '
+prebuildopts += 'for lib in "$EBROOTSOPLEX/lib/libsoplex*.a"; do ln -sf "$lib" "lib/"; done && '
+prebuildopts += 'for lib in "$EBROOTZIMPL/lib/libzimpl*.a"; do ln -sf "$lib" "lib/"; done && '
+
+# use SoPlex v2 as LP solver
+buildopts = 'LPS=spx2 '
+buildopts += 'MAKESOFTLINKS=false COMP=gnu OPT=opt '
+
+installopts = 'INSTALLDIR="%(installdir)s" '
+installopts += buildopts
+
+postinstallcmds = [
+    # add extra headers to installation directory
+    'cp "src/scip/misc.h" "%(installdir)s/include/scip/"',
+    # copy examples folder
+    'cp -r "examples" "%(installdir)s/"',
+]
+
+sanity_check_paths = {
+    'files': ['bin/scip', 'lib/liblpispx2.a', 'lib/libnlpi.cppad.a', 'lib/libobjscip.a', 'lib/libscip.a'],
+    'dirs': ['examples', 'include'],
+}
+
+sanity_check_commands = ["scip -h"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb
new file mode 100644
index 00000000000..309841532c7
--- /dev/null
+++ b/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'SoPlex'
+version = '2.2.1'
+
+homepage = 'https://soplex.zib.de/'
+description = """SoPlex is an optimization package for solving linear programming problems (LPs)
+based on an advanced implementation of the primal and dual revised simplex
+algorithm. It provides special support for the exact solution of LPs with
+rational input data. It can be used as a standalone solver reading MPS or LP
+format files via a command line interface as well as embedded into other
+programs via a C++ class library."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'scipopt'
+source_urls = [GITHUB_SOURCE]
+sources = ['release-%s.tar.gz' % version.replace('.', '')]
+checksums = ['6c2e89cd7c8910f8989f2a860fa0446641bd16d76eb87872f70974838486c9b1']
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('zlib', '1.2.12'),
+]
+
+skipsteps = ['configure']
+
+buildopts = "COMP=gnu OPT=opt"
+installopts = "INSTALLDIR=%(installdir)s"
+
+sanity_check_paths = {
+    'files': ['bin/soplex', 'lib/libsoplex.a'],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ["soplex | grep -q '%(name)s version %(version)s'"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..f193788ee27
--- /dev/null
+++ b/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'MakeCp'
+
+name = 'ZIMPL'
+version = '3.3.4'
+
+homepage = 'https://zimpl.zib.de/'
+description = """ZIMPL is a little language to translate the mathematical model of a problem
+into a linear or nonlinear (mixed-) integer mathematical program expressed in
+.lp or .mps file format which can be read and (hopefully) solved by a LP or MIP
+solver."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'scipopt'
+source_urls = ['https://zimpl.zib.de/download/']
+sources = [SOURCELOWER_TGZ]
+checksums = ['3362fb21524df459723d23f6e0c122ebdd684153a9cc991a2c7f5b2752a83eb2']
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('zlib', '1.2.12'),
+]
+
+files_to_copy = ['bin', 'lib', (['src/*.h'], 'include/zimpl')]
+
+postinstallcmds = [
+    "cd %(installdir)s/bin && ln -sf zimpl-%(version)s.* zimpl",
+    "cd %(installdir)s/lib && ln -sf libzimpl-%(version)s.*.a libzimpl.a",
+]
+
+sanity_check_paths = {
+    'files': ['bin/zimpl', 'lib/libzimpl.a'],
+    'dirs': ['include/zimpl'],
+}
+
+sanity_check_commands = ["zimpl -h"]
+
+moduleclass = 'math'

From e6a31ec9d8943baca685c27ca2cb15d8792e11fc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 1 Apr 2023 11:49:01 +0200
Subject: [PATCH 215/601] add dlm extension to R 4.2.1 + 4.2.2

---
 easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++
 easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
index 76fed434942..7829620a4a2 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
@@ -3466,6 +3466,9 @@ exts_list = [
     ('varhandle', '2.0.5', {
         'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'],
     }),
+    ('dlm', '1.1-6', {
+        'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'],
+    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
index dd02af827b6..ae739c4baf5 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
@@ -3537,6 +3537,9 @@ exts_list = [
     ('varhandle', '2.0.5', {
         'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'],
     }),
+    ('dlm', '1.1-6', {
+        'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'],
+    }),
 ]
 
 moduleclass = 'lang'

From 138942297c69c959e0f566eacdc930164a2d6169 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 1 Apr 2023 13:36:41 +0100
Subject: [PATCH 216/601] Remove LLVM builddep from TensorFlow

---
 .../t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb      | 1 -
 .../easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb      | 1 -
 .../easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb      | 1 -
 3 files changed, 3 deletions(-)

diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb
index 77b91670e2c..634b72ba92b 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb
@@ -17,7 +17,6 @@ builddependencies = [
     ('git', '2.33.1', '-nodocs'),
     ('pybind11', '2.7.1'),
     ('UnZip', '6.0'),
-    ('LLVM', '12.0.1'),  # for debugging with llvm-symbolizer, to be removed
 ]
 dependencies = [
     ('CUDA', '11.4.1', '', SYSTEM),
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb
index ae6d7df989c..e2c8fdba601 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb
@@ -16,7 +16,6 @@ builddependencies = [
     ('git', '2.33.1', '-nodocs'),
     ('pybind11', '2.7.1'),
     ('UnZip', '6.0'),
-    ('LLVM', '12.0.1'),  # for debugging with llvm-symbolizer, to be removed
 ]
 dependencies = [
     ('Python', '3.9.6'),
diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb
index 302f3bd958d..fdeaf3afa24 100644
--- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb
+++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb
@@ -16,7 +16,6 @@ builddependencies = [
     ('git', '2.33.1', '-nodocs'),
     ('pybind11', '2.7.1'),
     ('UnZip', '6.0'),
-    ('LLVM', '12.0.1'),  # for debugging with llvm-symbolizer, to be removed
 ]
 dependencies = [
     ('Python', '3.9.6'),

From 8e484911c20de913ec141c80eb0a008fc42153ae Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Sat, 1 Apr 2023 15:16:55 +0200
Subject: [PATCH 217/601] adding easyconfigs: R-transport-0.13-0-foss-2021b.eb

---
 .../R-transport-0.13-0-foss-2021b.eb          | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb

diff --git a/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb
new file mode 100644
index 00000000000..a025135e559
--- /dev/null
+++ b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb
@@ -0,0 +1,27 @@
+easyblock = 'RPackage'
+
+name = 'R-transport'
+local_rpkg = 'transport'
+version = '0.13-0'
+
+homepage = 'https://cran.r-project.org/package=transport'
+description = "transport: Computation of Optimal Transport Plans and Wasserstein Distances"
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = ['https://cran.r-project.org/src/contrib/']
+sources = ['%s_%%(version)s.tar.gz' % local_rpkg]
+checksums = ['c55efbdd93e36e92ef39e4b9529ee64c3c7ecb965d77ec9c469a7c56c93f5f57']
+
+dependencies = [
+    ('R', '4.1.2'),
+]
+
+options = {'modulename': local_rpkg}
+
+sanity_check_paths = {
+    'files': ['transport/R/transport', 'transport/libs/transport.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'math'

From c1098b2252419874205f7755469249348fe00de6 Mon Sep 17 00:00:00 2001
From: anselmicz <jakubkropacek@email.cz>
Date: Sat, 1 Apr 2023 15:23:19 +0200
Subject: [PATCH 218/601] adding easyconfigs:
 PostgreSQL-15.2-GCCcore-12.2.0.eb, libaio-0.3.113-GCCcore-12.2.0.eb,
 LZO-2.10-GCCcore-12.2.0.eb, jemalloc-5.3.0-GCCcore-12.2.0.eb,
 Judy-1.0.5-GCCcore-12.2.0.eb, MariaDB-10.11.2-GCC-12.2.0.eb,
 sysbench-1.0.20-GCC-12.2.0.eb

---
 .../j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb       | 34 ++++++++++
 .../jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb | 37 ++++++++++
 .../l/LZO/LZO-2.10-GCCcore-12.2.0.eb          | 27 ++++++++
 .../l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb | 39 +++++++++++
 .../m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb   | 68 +++++++++++++++++++
 .../PostgreSQL-15.2-GCCcore-12.2.0.eb         | 43 ++++++++++++
 .../s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb  | 39 +++++++++++
 7 files changed, 287 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..29e5a68235b
--- /dev/null
+++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'Judy'
+version = '1.0.5'
+
+homepage = 'http://judy.sourceforge.net/'
+description = "A C library that implements a dynamic array."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['http://downloads.sourceforge.net/judy']
+sources = ['%(name)s-%(version)s.tar.gz']
+patches = ['Judy-1.0.5_parallel-make.patch']  # fix Make dependencies, so parallel build also works
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('binutils', '2.39'),
+]
+checksums = [
+    'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb',  # Judy-1.0.5.tar.gz
+    '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009',  # Judy-1.0.5_parallel-make.patch
+]
+
+preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && "
+preconfigopts += "autoreconf -i && "
+
+configopts = '--enable-shared --enable-static'
+
+sanity_check_paths = {
+    'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT],
+    'dirs': ["share/man"]
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..aae1125cf83
--- /dev/null
+++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'jemalloc'
+version = '5.3.0'
+
+homepage = 'http://jemalloc.net'
+description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and
+ scalable concurrency support."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/jemalloc/jemalloc/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('binutils', '2.39'),
+]
+
+# From version 5.2.1 (or maybe earlier) it does no longer build,
+# nor try to install, documentation if xsltproc is missing.
+# So we can use normal installation.
+preconfigopts = "./autogen.sh && "
+configopts = "--with-version=%(version)s-0-g0000 "  # build with version info
+
+sanity_check_paths = {
+    'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT,
+              'include/jemalloc/jemalloc.h'],
+    'dirs': [],
+}
+
+# jemalloc can be used via $LD_PRELOAD, but we don't enable this by
+# default, you need to opt-in to it
+# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..e1ced572aa5
--- /dev/null
+++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'LZO'
+version = '2.10'
+
+homepage = 'https://www.oberhumer.com/opensource/lzo/'
+description = "Portable lossless data compression library"
+
+source_urls = [homepage + 'download/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072']
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [('binutils', '2.39')]
+
+configopts = '--enable-shared'
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT],
+    'dirs': ['include']
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..64d50b5219d
--- /dev/null
+++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'MakeCp'
+
+name = 'libaio'
+version = '0.3.113'
+_libversion = '1.0.2'
+
+homepage = 'https://pagure.io/libaio'
+description = "Asynchronous input/output library that uses the kernels native interface."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['1c561c20670c5c09cc8437a622008c0693c6a7816c1f30332da3796953b2f454']
+
+builddependencies = [('binutils', '2.39')]
+
+_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion)
+
+files_to_copy = [
+    (["src/libaio.a", "src/%s" % _soname], "lib"),
+    (["src/libaio.h"], "include"),
+]
+
+# links to the shared library with generic names
+_solinks = [
+    "libaio.%s" % SHLIB_EXT,
+    "libaio.%s.1" % SHLIB_EXT,
+]
+
+postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks]
+
+sanity_check_paths = {
+    'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb
new file mode 100644
index 00000000000..37fce889bdc
--- /dev/null
+++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb
@@ -0,0 +1,68 @@
+easyblock = 'CMakeMake'
+
+name = 'MariaDB'
+version = '10.11.2'
+
+homepage = 'https://mariadb.org/'
+description = """MariaDB is an enhanced, drop-in replacement for MySQL.
+Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+source_urls = [
+    'https://archive.mariadb.org/mariadb-%(version)s/source/',
+    'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch']
+checksums = [
+    {'mariadb-10.11.2.tar.gz': '1c89dee0caed0f68bc2a1d203eb98a123150e6a179f6ee0f1fc0ba3f08dc71dc'},
+    {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('libaio', '0.3.113'),
+]
+
+dependencies = [
+    ('ncurses', '6.3'),
+    ('zlib', '1.2.12'),
+    ('LZO', '2.10'),        # optional
+    ('lz4', '1.9.4'),       # optional
+    ('XZ', '5.2.7'),        # optional
+    ('jemalloc', '5.3.0'),  # optional
+    ('snappy', '1.1.9'),    # needed by RocksDB; optional for InnoDB
+    ('libxml2', '2.10.3'),  # needed by Connect XML
+    ('Boost', '1.81.0'),    # needed by OQGraph
+    ('Judy', '1.0.5'),      # needed by OQGraph
+    ('PCRE2', '10.40'),
+    ('OpenSSL', '1.1', '', SYSTEM),     # runtime dep for mysql and PCRE2 for mysqltest
+]
+
+separate_build_dir = True
+
+configopts = "-DCMAKE_BUILD_TYPE=Release "
+configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' "  # Linking fails with default gold linker
+configopts += "-DMYSQL_MAINTAINER_MODE=OFF "  # disabled to not treat warnings as errors (-Werror)
+configopts += "-DWITH_PCRE=auto "  # External download sometimes fails so we build PCRE2 directly.
+configopts += "-DWITH_ZLIB=system "
+configopts += "-DWITH_EMBEDDED_SERVER=ON "  # for libmysqld.so & co
+configopts += "-DWITH_SAFEMALLOC=OFF "  # Disable memory debugger with jemalloc
+
+sanity_check_commands = ["mysql --help", "mysqltest --help"]
+
+sanity_check_paths = {
+    'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT,
+              'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT,
+              'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'],
+    'dirs': ['include', 'share'],
+}
+
+modextrapaths = {'PATH': 'scripts'}
+
+# Ensure that jemalloc does not use transparent hugepages.
+# Database workloads with THP can cause memory bloat, potentially hiting OOM errors.
+modextravars = {'MALLOC_CONF': 'thp:never'}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..14b35601d98
--- /dev/null
+++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb
@@ -0,0 +1,43 @@
+easyblock = 'ConfigureMake'
+
+name = 'PostgreSQL'
+version = '15.2'
+
+homepage = 'https://www.postgresql.org/'
+description = """PostgreSQL is a powerful, open source object-relational database system.
+ It is fully ACID compliant, has full support for foreign keys,
+ joins, views, triggers, and stored procedures (in multiple languages).
+ It includes most SQL:2008 data types, including INTEGER,
+ NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP.
+ It also supports storage of binary large objects, including pictures,
+ sounds, or video. It has native programming interfaces for C/C++, Java,
+ .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['eccd208f3e7412ad7bc4c648ecc87e0aa514e02c24a48f71bf9e46910bf284ca']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+    ('Perl', '5.36.0'),
+    ('Python', '3.10.8'),
+]
+
+dependencies = [
+    ('libreadline', '8.2'),
+    ('zlib', '1.2.12'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+configopts = '--with-python --with-openssl'
+
+sanity_check_paths = {
+    'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT],
+    'dirs': ['share/postgresql'],
+}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
new file mode 100644
index 00000000000..45c70aeb5f0
--- /dev/null
+++ b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'sysbench'
+version = '1.0.20'
+
+homepage = 'https://github.com/akopytov/sysbench'
+description = """sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT.
+ It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex
+ workloads that do not involve a database server."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+github_account = 'akopytov'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['e8ee79b1f399b2d167e6a90de52ccc90e52408f7ade1b9b7135727efe181347f']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('pkgconf', '1.9.3'),
+]
+
+dependencies = [
+    ('libtool', '2.4.7'),
+    ('MariaDB', '10.11.2'),
+    ('PostgreSQL', '15.2'),  # optional
+]
+
+preconfigopts = './autogen.sh &&'
+configopts = '--with-pgsql '  # optional
+
+sanity_check_paths = {
+    'files': ['bin/sysbench'],
+    'dirs': ['bin', 'share']
+}
+
+sanity_check_commands = ['sysbench --help']
+
+moduleclass = 'tools'

From 830a5e10ecab26bbf51356092490a9d74cabced0 Mon Sep 17 00:00:00 2001
From: anselmicz <jakubkropacek@email.cz>
Date: Sat, 1 Apr 2023 15:46:50 +0200
Subject: [PATCH 219/601] adding easyconfigs: Vim-9.0.1434-GCCcore-12.2.0.eb

---
 .../v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb      | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..3ba63172bd8
--- /dev/null
+++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'Vim'
+version = '9.0.1434'
+
+homepage = 'http://www.vim.org'
+description = """ Vim is an advanced text editor that seeks to provide the power 
+ of the de-facto Unix editor 'Vi', with a more complete feature set. """
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/vim/vim/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['f7a43d6f2c08c4d76c5ceb9ab6603fe2d87d56c1162934525cf46362ef8a4e65']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('Perl', '5.36.0'),
+    ('PCRE', '8.45')
+]
+
+configopts = '--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes'
+
+sanity_check_paths = {
+    'files': ['bin/vim', 'bin/vimtutor', 'bin/xxd'],
+    'dirs': ['bin', 'share'],
+}
+
+sanity_check_commands = ['vim --version']
+
+moduleclass = 'tools'

From a1ca871894643db6784f08caaddad758181c2105 Mon Sep 17 00:00:00 2001
From: anselmicz <jakubkropacek@email.cz>
Date: Sat, 1 Apr 2023 16:05:43 +0200
Subject: [PATCH 220/601] adding easyconfigs: nvtop-3.0.1-GCCcore-12.2.0.eb

---
 .../n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb     | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..1d50e1ff0c1
--- /dev/null
+++ b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'CMakeMake'
+
+name = 'nvtop'
+version = '3.0.1'
+
+homepage = 'https://github.com/Syllo/nvtop'
+description = 'htop-like GPU usage monitor'
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/Syllo/nvtop/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['f61ecbe3a30a216706c16fc177d3b840e7d7deccf87b048d59f95f230d591a53']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency.
+dependencies = [
+    ('ncurses', '6.3'),
+    ('libdrm', '2.4.114'),
+]
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['bin/nvtop'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["nvtop --help"]
+
+moduleclass = 'tools'

From e50f8595d541a41645942e3d8c7a3666b4989de8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 1 Apr 2023 16:25:52 +0200
Subject: [PATCH 221/601] adding easyconfigs:
 CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb

---
 .../CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb       | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..2e0b17c5c7e
--- /dev/null
+++ b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,29 @@
+easyblock = 'RPackage'
+
+name = 'CopyKAT'
+local_commit = 'b795ff7'
+version = '1.1.0'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/navinlabcode/copykat'
+description = """CopyKAT: Inference of genomic copy number and subclonal structure of human tumors from
+ high-throughput single cell RNAseq data"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/navinlabcode/copykat/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['8b4e39591ad81d146873694b8311607bfec88ad57df8daa9244b2e31904193b5']
+
+dependencies = [
+    ('R', '4.2.1'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['%(namelower)s'],
+}
+
+options = {'modulename': '%(namelower)s'}
+
+moduleclass = 'bio'

From 4d0bbda30796bedb24df34b12f8fe897e8853c56 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 1 Apr 2023 20:50:03 +0200
Subject: [PATCH 222/601] adding easyconfigs: powerlaw-1.5-foss-2022a.eb

---
 .../p/powerlaw/powerlaw-1.5-foss-2022a.eb     | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb b/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb
new file mode 100644
index 00000000000..76d53174915
--- /dev/null
+++ b/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb
@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'powerlaw'
+version = '1.5'
+
+homepage = 'http://www.github.com/jeffalstott/powerlaw'
+description = "powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_PY3_WHL]
+checksums = ['633a669573d9fd663d2f452f121117f2d6b2f2c502eca532f9355f733abfec96']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+moduleclass = 'math'

From 4bd1e64e58e4bf9358a2809b4ce8c8e8c0a6697d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 1 Apr 2023 20:55:50 +0200
Subject: [PATCH 223/601] {data}[foss/2021a] scib v1.1.3, Deprecated v1.2.13 w/
 Python 3.9.5

---
 .../Deprecated-1.2.13-foss-2021a.eb           | 29 ++++++++++++++
 .../s/scib/scib-1.1.3-foss-2021a.eb           | 39 +++++++++++++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb
 create mode 100644 easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb

diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb
new file mode 100644
index 00000000000..37b1d866da5
--- /dev/null
+++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb
@@ -0,0 +1,29 @@
+# author: Denis Kristak (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'Deprecated'
+version = '1.2.13'
+
+homepage = 'https://github.com/tantale/deprecated'
+description = "If you need to mark a function or a method as deprecated, you can use the @deprecated decorator."
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+dependencies = [
+    ('Python', '3.9.5'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('wrapt', '1.15.0', {
+        'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'],
+    }),
+    (name, version, {
+        'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb
new file mode 100644
index 00000000000..ffd4fc238c0
--- /dev/null
+++ b/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb
@@ -0,0 +1,39 @@
+# author: Denis Kristak (INUITS)
+easyblock = 'PythonPackage'
+
+name = 'scib'
+version = '1.1.3'
+
+homepage = 'https://github.com/theislab/scib'
+description = "Benchmarking atlas-level data integration in single-cell genomics."
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['2b59d7c291e99bd508b91d73ff07fc4961fded37b06089e4f19fc5ee9cc4e3f3']
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('Seaborn', '0.11.2'),
+    ('numba', '0.53.1'),
+    ('scanpy', '1.8.1'),
+    ('h5py', '3.2.1'),
+    ('scikit-learn', '0.24.2'),
+    ('scikit-misc', '0.1.4'),
+    ('leidenalg', '0.8.7'),
+    ('umap-learn', '0.5.3'),
+    ('pydot', '1.4.2'),
+    ('igraph', '0.9.4'),
+    ('python-igraph', '0.9.6'),
+    ('Deprecated', '1.2.13'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+preinstallopts = "sed -i 's|igraph>=0.10|python-igraph>=0.9.6|g' setup.cfg && "
+preinstallopts += "sed -i 's|louvain>=0.8||g' setup.cfg && "
+
+moduleclass = 'data'

From 9c62488c0fdfb3efae9e782596c9a427031ce7a3 Mon Sep 17 00:00:00 2001
From: Jasper <65227842+jfgrimm@users.noreply.github.com>
Date: Mon, 3 Apr 2023 10:52:02 +0100
Subject: [PATCH 224/601] Update easybuild/easyconfigs/z/zsh/zsh-5.9.eb

Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com>
---
 easybuild/easyconfigs/z/zsh/zsh-5.9.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
index 574b12cb58d..ff8bd3f2190 100644
--- a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
+++ b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
@@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_XZ]
 checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5']
 
 osdependencies = [
-    ('ncurses-devel', 'ncurses-dev'),
+    ('ncurses-devel', 'libncurses-dev'),
 ]
 
 configopts = '--with-tcsetpgrp'  # needed to build in non-login shells

From d86a6c921ab7790c6bcd1b9040e5e8a1f5720101 Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Mon, 3 Apr 2023 12:07:41 +0200
Subject: [PATCH 225/601] Add CUDA to OpenMM

---
 .../easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb      | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
index 47d3bdbfaf5..87db305f12a 100644
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
@@ -29,10 +29,15 @@ dependencies = [
     ('Python', '3.10.4'),
     ('SciPy-bundle', '2022.05'),
     ('SWIG', '4.0.2'),
+    ('CUDA', '11.7.0', '', SYSTEM),
 ]
 
-pretestopts = " CTEST_OUTPUT_ON_FAILURE=1"
-local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)"
+# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc,
+# Otherwise they will use the wrong path: `/usr/bin/nvcc`
+pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && '
+pretestopts += " CTEST_OUTPUT_ON_FAILURE=1"
+# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set
+local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)"
 runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern
 
 preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '

From 956625cee5b456723e83224ae2ac53de85f0e5ee Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Mon, 3 Apr 2023 12:10:11 +0200
Subject: [PATCH 226/601] Fix comment

---
 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
index 87db305f12a..3a717e67758 100644
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
@@ -33,7 +33,7 @@ dependencies = [
 ]
 
 # Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc,
-# Otherwise they will use the wrong path: `/usr/bin/nvcc`
+# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc`
 pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && '
 pretestopts += " CTEST_OUTPUT_ON_FAILURE=1"
 # Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set

From 15f5792d795e9a0b8b1bd1b1eb06f64ab575b4e5 Mon Sep 17 00:00:00 2001
From: guacke <guillaume.acke@ugent.be>
Date: Mon, 3 Apr 2023 14:06:00 +0200
Subject: [PATCH 227/601] adding easyconfigs:
 Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb

---
 .../Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..b63f52585f9
--- /dev/null
+++ b/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PackedBinary'
+
+name = 'Blender'
+version = '3.5.0'
+versionsuffix = '-linux-x86_64-CUDA-%(cudaver)s'
+
+homepage = 'https://www.blender.org/'
+description = """Blender is the free and open source 3D creation suite. It supports
+ the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering,
+ compositing and motion tracking, even video editing and game creation."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/']
+sources = ['blender-%(version)s-linux-x64.tar.xz']
+checksums = ['a74d52822d5753a1ffb617ac764bbacc12a4a6dec4c2b91e90cc2935a40fff68']
+
+dependencies = [
+    ('CUDA', '11.7.0')
+]
+
+sanity_check_paths = {
+    'files': ['blender', 'blender-softwaregl'],
+    'dirs': ['%(version_major_minor)s'],
+}
+
+sanity_check_commands = ["blender --help"]
+
+moduleclass = 'vis'

From d4392f22296520cf76ed4fb27b4c5c822a7701a2 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 4 Apr 2023 10:34:35 +0200
Subject: [PATCH 228/601] adding easyconfigs: FunGAP-1.1.1-foss-2022a.eb and
 patches: FunGAP-1.1.1_fix-snap-detection.patch,
 FunGAP-1.1.1_relax-dependency-checks.patch,
 FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch,
 FunGAP-1.1.1_fix-maker-exes.patch,
 FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch

---
 .../f/FunGAP/FunGAP-1.1.1-foss-2022a.eb       | 91 +++++++++++++++++++
 ...1.1_fix-augustus-calls-in-runbreaker.patch | 54 +++++++++++
 .../FunGAP/FunGAP-1.1.1_fix-maker-exes.patch  | 20 ++++
 .../FunGAP-1.1.1_fix-snap-detection.patch     | 61 +++++++++++++
 ...FunGAP-1.1.1_relax-dependency-checks.patch | 29 ++++++
 ..._replace-deprecated-pa-repeatmodeler.patch | 22 +++++
 6 files changed, 277 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch
 create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch
 create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch
 create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch
 create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch

diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
new file mode 100644
index 00000000000..5c1328194ce
--- /dev/null
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
@@ -0,0 +1,91 @@
+easyblock = 'Tarball'
+
+name = 'FunGAP'
+version = '1.1.1'
+
+homepage = 'https://github.com/CompSynBioLab-KoreaUniv/FunGAP'
+description = "Fungal Genome Annotation Pipeline using evidence-based gene model evaluation."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# Tag v1.1.1 points to an old commit still in v1.1.0
+# pull correct sources from specific commit
+_commit = '924f3ba080f98cbf181b0b21601e095619479ce6'
+
+source_urls = ['https://github.com/CompSynBioLab-KoreaUniv/FunGAP/archive']
+sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}]
+patches = [
+    'FunGAP-%(version)s_fix-snap-detection.patch',
+    'FunGAP-%(version)s_relax-dependency-checks.patch',
+    'FunGAP-%(version)s_replace-deprecated-pa-repeatmodeler.patch',
+    'FunGAP-%(version)s_fix-maker-exes.patch',
+    'FunGAP-%(version)s_fix-augustus-calls-in-runbreaker.patch',
+]
+checksums = [
+    {'FunGAP-1.1.1.tar.gz': '3d827c4b11452afdd51b71766e0e3193b7efad31db4536606115f2cac0b964c8'},
+    {'FunGAP-1.1.1_fix-snap-detection.patch': 'f782224ce186e1e2d8953898122b79d616f8a749b00ec662ec5a3fa1903550fa'},
+    {'FunGAP-1.1.1_relax-dependency-checks.patch': '73f9ae2a20cf03c34f852642a28d3b7e9858250f653ff1e711c3c9a56ae2fd77'},
+    {'FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch':
+     'c528aab74a070d6eedc9ff2097b6149e8d36759b9ff93c46302994179a38a774'},
+    {'FunGAP-1.1.1_fix-maker-exes.patch': 'de344cf45dad047ab46a17462e19ce0789a89071c1484cbdedd9d898f9601bd0'},
+    {'FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch':
+     '150b6f79f95d0c8abece42231c5dcedf8610a811db9cc63ac6cc047f0dcfdc64'},
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Perl', '5.34.1'),
+    ('AUGUSTUS', '3.5.0'),
+    ('BamTools', '2.5.2'),
+    ('bcbio-gff', '0.7.0'),
+    ('BRAKER', '2.1.6'),
+    ('BUSCO', '5.4.5'),
+    ('HISAT2', '2.2.1'),
+    ('MAKER', '3.01.04'),
+    ('matplotlib', '3.5.2'),
+    ('networkx', '2.8.4'),
+    ('PfamScan', '1.6'),
+    ('RepeatModeler', '2.0.4'),
+    ('SAMtools', '1.16.1'),
+    ('SNAP-HMM', '20221022'),
+    ('Trinity', '2.15.1'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('markdown2', '2.4.8', {
+        'checksums': ['90475aca3d9c8e7df6d70c51de5bbbe9edf7fcf6a380bd1044d321500f5445da'],
+    }),
+]
+
+postinstallcmds = [
+    # execute set_dependencies.py, which creates configuration file and runs some quick tests
+    ("cd %(installdir)s && ./set_dependencies.py --pfam_db_path /databases/bio/Pfam-35 "
+     "--genemark_path $EBROOTGENEMARKMINET --maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin"),
+]
+
+sanity_check_paths = {
+    'files': ['fungap.py'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+modextrapaths = {
+    'PATH': '',
+    'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages']
+}
+
+modextravars = {
+    'FUNGAP_DIR': '%(installdir)s',
+}
+
+sanity_check_commands = [
+    ('fungap.py', '--help'),
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch
new file mode 100644
index 00000000000..a245df16275
--- /dev/null
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch
@@ -0,0 +1,54 @@
+Set paths to AUGUSTUS installation preferably from its environment variables
+Fix location of getAnnoFastaFromJoingenes.py script from AUGUSTUS
+see https://github.com/CompSynBioLab-KoreaUniv/FunGAP/pull/98
+author: Alex Domingo (Vrije Universirteit Brussel)
+--- run_braker.py.orig	2023-04-03 12:07:35.178272000 +0200
++++ run_braker.py	2023-04-03 12:24:48.713953000 +0200
+@@ -124,8 +124,19 @@
+         logger_time.debug('START: BRAKER')
+ 
+         if not os.path.exists(gff3_braker):
+-            augustus_config_path = os.path.join(
+-                os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../config')
++            augustus_bin_path = os.environ[
++                'AUGUSTUS_BIN_PATH'
++            ] or os.path.dirname(D_CONF['AUGUSTUS_PATH'])
++            augustus_config_path = os.environ[
++                'AUGUSTUS_CONFIG_PATH'
++            ] or os.path.join(
++                os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../config'
++            )
++            augustus_scripts_path = os.environ[
++                'AUGUSTUS_SCRIPTS_PATH'
++            ] or os.path.join(
++                os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../scripts'
++            )
+             config_species = os.path.join(
+                 augustus_config_path, 'species', prefix)
+             species = prefix
+@@ -140,7 +151,6 @@
+             bamtools_path = os.path.dirname(D_CONF['BAMTOOLS_PATH'])
+             genemark_path = os.path.dirname(D_CONF['GENEMARK_PATH'])
+             samtools_path = os.path.dirname(D_CONF['SAMTOOLS_PATH'])
+-            augustus_scripts_path = os.path.dirname(D_CONF['AUGUSTUS_PATH'])
+             working_dir = os.path.join(output_dir, prefix)
+             if not os.path.exists(working_dir):
+                 os.mkdir(working_dir)
+@@ -153,7 +163,7 @@
+                     braker_bin, fungus_flag, num_cores, adjusted_assembly,
+                     bam_file, species, augustus_config_path, bamtools_path,
+                     genemark_path, samtools_path, working_dir,
+-                    translation_table, augustus_scripts_path, log_braker))
++                    translation_table, augustus_bin_path, log_braker))
+             logger_txt.debug('[Run] %s', command1)
+             os.system(command1)
+ 
+@@ -165,7 +175,7 @@
+ 
+             augustus_dir = os.path.dirname(D_CONF['AUGUSTUS_PATH'])
+             get_anno_script = os.path.join(
+-                augustus_dir, 'getAnnoFastaFromJoingenes.py')
++                augustus_scripts_path, 'getAnnoFastaFromJoingenes.py')
+             if not os.path.exists(get_anno_script):
+                 get_anno_script = os.path.join(
+                     augustus_dir,
diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch
new file mode 100644
index 00000000000..b172ca04d47
--- /dev/null
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch
@@ -0,0 +1,20 @@
+The paths to MAKER executables set by MAKER are already correct, avoid
+tampering with them.
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- run_maker.py.orig	2023-03-21 09:19:05.057679000 +0100
++++ run_maker.py	2023-03-21 09:19:49.143408491 +0100
+@@ -463,14 +463,6 @@
+     replace('maker_opts.ctl', 'protein_pass=0', 'protein_pass=1')
+     replace('maker_opts.ctl', 'rm_pass=0', 'rm_pass=1')
+ 
+-    # Program paths
+-    for program in [
+-            'makeblastdb', 'blastn', 'blastx', 'tblastx', 'RepeatMasker',
+-            'exonerate', 'snap', 'augustus', 'tRNAscan-SE', 'snoscan']:
+-        replace('maker_exe.ctl', '{}='.format(program), '{}={}'.format(
+-            program, os.path.join(os.path.dirname(maker_bin), program)
+-        ))
+-
+     # Last run, keep_preds=1
+     if version == '4':
+         replace('maker_opts.ctl', 'keep_preds=0', 'keep_preds=1')
diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch
new file mode 100644
index 00000000000..c8dd7ab6262
--- /dev/null
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch
@@ -0,0 +1,61 @@
+Fix detection of fathom, forge and hmm-assembler.pl, which are not part of MAKER but SNAP
+see https://github.com/CompSynBioLab-KoreaUniv/FunGAP/pull/97
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- set_dependencies.py.orig	2023-03-16 15:27:00.506475000 +0100
++++ set_dependencies.py	2023-03-16 15:31:31.102674857 +0100
+@@ -44,6 +44,10 @@
+         help='Maker bin path'
+     )
+     parser.add_argument(
++        '-s', '--snap_path', nargs=1, required=True,
++        help='SNAP-HMM bin path'
++    )
++    parser.add_argument(
+         '-r', '--with_repeat_modeler', nargs='?', default='',
+         help='User-defined RepeatModeler bin path'
+     )
+@@ -76,6 +80,7 @@
+     pfam_db_path = os.path.abspath(args.pfam_db_path[0])
+     i_genemark_path = os.path.abspath(args.genemark_path[0])
+     i_maker_path = os.path.abspath(args.maker_path[0])
++    i_snap_path = os.path.abspath(args.snap_path[0])
+     if args.with_repeat_modeler:
+         with_repeat_modeler = os.path.abspath(args.with_repeat_modeler)
+     else:
+@@ -104,8 +109,9 @@
+         pfam_scan_path, blastp_path, blastn_path, blastx_path,
+         makeblastdb_path, samtools_path, bamtools_path, augustus_path
+     ) = get_path(
+-        i_genemark_path, i_maker_path, with_repeat_modeler, with_augustus,
+-        with_hisat2, with_trinity, with_braker, with_busco, with_pfam_scan
++        i_genemark_path, i_maker_path, i_snap_path, with_repeat_modeler,
++        with_augustus, with_hisat2, with_trinity, with_braker, with_busco,
++        with_pfam_scan
+     )
+     check_working(
+         genemark_path, gmhmme3_path, probuild_path, build_database_path,
+@@ -159,8 +165,9 @@
+ 
+ 
+ def get_path(
+-        i_genemark_path, i_maker_path, with_repeat_modeler, with_augustus,
+-        with_hisat2, with_trinity, with_braker, with_busco, with_pfam_scan):
++        i_genemark_path, i_maker_path, i_snap_path, with_repeat_modeler,
++        with_augustus, with_hisat2, with_trinity, with_braker, with_busco,
++        with_pfam_scan):
+     '''Get path'''
+     print('\n** Checking the installed locations of dependencies **\n')
+ 
+@@ -198,9 +205,9 @@
+     gff3_merge_path = check_binary('Maker', i_maker_path, 'gff3_merge')
+     fasta_merge_path = check_binary('Maker', i_maker_path, 'fasta_merge')
+     maker2zff_path = check_binary('Maker', i_maker_path, 'maker2zff')
+-    fathom_path = check_binary('Snap', i_maker_path, 'fathom')
+-    forge_path = check_binary('Snap', i_maker_path, 'forge')
+-    hmm_assembler_path = check_binary('Snap', i_maker_path, 'hmm-assembler.pl')
++    fathom_path = check_binary('Snap', i_snap_path, 'fathom')
++    forge_path = check_binary('Snap', i_snap_path, 'forge')
++    hmm_assembler_path = check_binary('Snap', i_snap_path, 'hmm-assembler.pl')
+     build_database_path = check_binary(
+         'RepeatModeler (BuildDatabase)', with_repeat_modeler, 'BuildDatabase',
+     )
diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch
new file mode 100644
index 00000000000..68d88fe47b2
--- /dev/null
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch
@@ -0,0 +1,29 @@
+Disable too strict check on version of AUGUSTUS and the GeneMark key in the
+home directory of the user
+author: Alex Domingo (Vrije Universiteit Brusel)
+--- set_dependencies.py.orig	2023-03-16 15:50:03.802522000 +0100
++++ set_dependencies.py	2023-03-16 15:50:28.562603082 +0100
+@@ -284,15 +284,15 @@
+     check_working_internal(samtools_path, [samtools_path, '--help'])
+     check_working_internal(bamtools_path, [bamtools_path, '--help'])
+     check_working_internal(augustus_path, [augustus_path, '--help'])
+-    check_augustus_version(augustus_path)
++    # check_augustus_version(augustus_path)
+ 
+-    # For GeneMark, check the .gm_key
+-    home_path = os.path.expanduser('~')
+-    if not os.path.exists(os.path.join(home_path, '.gm_key')):
+-        sys.exit(
+-            '\n[ERROR] You do not have .gm_key in your home directory.\n'
+-            'Check https://wiki.gacrc.uga.edu/wiki/GeneMark'
+-        )
++    # # For GeneMark, check the .gm_key
++    # home_path = os.path.expanduser('~')
++    # if not os.path.exists(os.path.join(home_path, '.gm_key')):
++    #     sys.exit(
++    #         '\n[ERROR] You do not have .gm_key in your home directory.\n'
++    #         'Check https://wiki.gacrc.uga.edu/wiki/GeneMark'
++    #     )
+ 
+ def check_augustus_version(augustus_path):
+     '''Check Augustus version 3.3.3'''
diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch
new file mode 100644
index 00000000000..8d75c3a8ae6
--- /dev/null
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch
@@ -0,0 +1,22 @@
+Replace deprecated -pa option in newer versions of RepeatModeler with -threads
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- run_repeat_modeler.py.orig	2023-03-17 09:23:21.857374000 +0100
++++ run_repeat_modeler.py	2023-03-17 09:24:17.655942000 +0100
+@@ -73,7 +73,7 @@
+ 
+     # BuildDatabase -name Choanephora_cucurbitarum
+     # ../Choanephora_cucurbitarum_assembly.fna
+-    # RepeatModeler -database Choanephora_cucurbitarum -pa 25
++    # RepeatModeler -database Choanephora_cucurbitarum -threads 25
+ 
+     # Get repeat model
+     repeat_lib = os.path.join(output_dir, '*', 'consensi.fa.classified')
+@@ -89,7 +89,7 @@
+         os.system(command1)
+ 
+         log_file2 = os.path.join(log_dir, 'repeat_modeler.log')
+-        command2 = '{} -database {} -pa {} > {} 2>&1'.format(
++        command2 = '{} -database {} -threads {} > {} 2>&1'.format(
+             repeatmodeler_bin, genome_assembly, num_cores, log_file2
+         )
+         logger_txt.debug('[Run] %s', command2)

From 5674fb3c42e04f0acf3594049f5457ff90872d39 Mon Sep 17 00:00:00 2001
From: Adam Huffman <verdurin@users.noreply.github.com>
Date: Tue, 4 Apr 2023 11:52:18 +0100
Subject: [PATCH 229/601] Update spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb

Use `SYSTEM` for a binary dep.
---
 .../s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
index 171697664e9..e5b551b446f 100644
--- a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb
@@ -26,7 +26,7 @@ dependencies = [
     ('networkx', '2.6.3'),
     ('tqdm', '4.62.3'),
     ('scikit-learn', '1.0.1'),
-    ('CUDA', '11.4.1', '', True),
+    ('CUDA', '11.4.1', '', SYSTEM),
     ('TensorFlow', '2.7.1', versionsuffix),
 ]
 

From b42386eb64174af96d137f70c1c68fb0761b50eb Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 4 Apr 2023 16:49:25 +0200
Subject: [PATCH 230/601] Add patch to resolve tree-vectorize issue

---
 .../o/OpenMM/OpenMM-8.0.0-foss-2022a.eb          |  6 +++++-
 .../OpenMM-8.0.0_add_no_tree_vectorize.patch     | 16 ++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch

diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
index 3a717e67758..52869cc7ee4 100644
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
@@ -18,7 +18,11 @@ toolchainopts = {'opt': True}
 
 source_urls = ['https://github.com/openmm/openmm/archive/']
 sources = ['%(version)s.tar.gz']
-checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e']
+patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch']
+checksums = [
+    'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e',  # 8.0.0.tar.gz 
+    '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd',  # OpenMM-8.0.0_add_no_tree_vectorize.patch
+]
 
 builddependencies = [
     ('CMake', '3.23.1'),
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch
new file mode 100644
index 00000000000..e3fb0d99579
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch
@@ -0,0 +1,16 @@
+# This patch resolves the tree vectorizatior error that appears when "-march" is used with GCC 11.3.0:
+#   .../openmm-8.0.0/platforms/common/src/CommonKernels.cpp:5055:6: internal compiler error: in vect_get_vec_defs_for_operand, at tree-vect-stmts.c:1450
+#   5055 | void CommonCalcGayBerneForceKernel::sortAtoms() {
+# Author: maxim-masterov (SURF)
+
+diff -Nru openmm-8.0.0.orig/platforms/common/src/CommonKernels.cpp openmm-8.0.0/platforms/common/src/CommonKernels.cpp
+--- openmm-8.0.0.orig/platforms/common/src/CommonKernels.cpp	2023-03-29 10:08:28.765461000 +0200
++++ openmm-8.0.0/platforms/common/src/CommonKernels.cpp	2023-04-04 15:55:17.152316000 +0200
+@@ -5052,6 +5052,7 @@
+     sortAtoms();
+ }
+ 
++__attribute__((optimize("no-tree-vectorize")))
+ void CommonCalcGayBerneForceKernel::sortAtoms() {
+     // Sort the list of atoms by type to avoid thread divergence.  This is executed every time
+     // the atoms are reordered.

From 2b69ad1e3bd3028fc54a629ebbe2aa0a68e67f6f Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 4 Apr 2023 17:17:12 +0200
Subject: [PATCH 231/601] Fix style

---
 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
index 52869cc7ee4..4d937a03a22 100644
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
@@ -20,7 +20,7 @@ source_urls = ['https://github.com/openmm/openmm/archive/']
 sources = ['%(version)s.tar.gz']
 patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch']
 checksums = [
-    'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e',  # 8.0.0.tar.gz 
+    'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e',  # 8.0.0.tar.gz
     '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd',  # OpenMM-8.0.0_add_no_tree_vectorize.patch
 ]
 

From 32cd82fa0e95be9360464d58f9696c7900d6a6f5 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 4 Apr 2023 18:18:50 +0200
Subject: [PATCH 232/601] install Pfam database if missing in FunGAP
 installation directory

---
 .../f/FunGAP/FunGAP-1.1.1-foss-2022a.eb         | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
index 5c1328194ce..171e5c1d38e 100644
--- a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
@@ -64,10 +64,23 @@ exts_list = [
     }),
 ]
 
+# FunGAP needs the Pfam database (280 MB download, 1.5 GB on disk)
+# if it's already available in your system change _pfam_db_dir to its location
+_pfam_db_dir = '%(installdir)s/db'
+_pfam_db_url = 'https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release'
+_pfam_db_install_cmds = [
+    "mkdir -p %s" % _pfam_db_dir,
+    "wget -P %s %s/{Pfam-A.hmm.gz,Pfam-A.hmm.dat.gz,active_site.dat.gz}" % (_pfam_db_dir, _pfam_db_url),
+    "gzip -d %s/*.gz" % _pfam_db_dir,
+    "hmmpress %s/Pfam-A.hmm" % _pfam_db_dir,
+]
+
 postinstallcmds = [
+    # install Pfam DB if missing
+    "if [ ! -f %s/Pfam-A.hmm ]; then %s; fi" % (_pfam_db_dir, " && ".join(_pfam_db_install_cmds)), 
     # execute set_dependencies.py, which creates configuration file and runs some quick tests
-    ("cd %(installdir)s && ./set_dependencies.py --pfam_db_path /databases/bio/Pfam-35 "
-     "--genemark_path $EBROOTGENEMARKMINET --maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin"),
+    ("cd %%(installdir)s && ./set_dependencies.py --pfam_db_path %s --genemark_path $EBROOTGENEMARKMINET "
+     "--maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin" % _pfam_db_dir),
 ]
 
 sanity_check_paths = {

From 6482e680f92611aaaefd49b5fa63ca2e87f492e8 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 4 Apr 2023 18:47:38 +0200
Subject: [PATCH 233/601] remove trailing spaces in FunGAP-1.1.1-foss-2022a.eb

---
 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
index 171e5c1d38e..a974e867d2b 100644
--- a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
@@ -77,7 +77,7 @@ _pfam_db_install_cmds = [
 
 postinstallcmds = [
     # install Pfam DB if missing
-    "if [ ! -f %s/Pfam-A.hmm ]; then %s; fi" % (_pfam_db_dir, " && ".join(_pfam_db_install_cmds)), 
+    "if [ ! -f %s/Pfam-A.hmm ]; then %s; fi" % (_pfam_db_dir, " && ".join(_pfam_db_install_cmds)),
     # execute set_dependencies.py, which creates configuration file and runs some quick tests
     ("cd %%(installdir)s && ./set_dependencies.py --pfam_db_path %s --genemark_path $EBROOTGENEMARKMINET "
      "--maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin" % _pfam_db_dir),

From 9f81fbea418d2f6ffaac075a03db0a5f3fc19e01 Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Wed, 5 Apr 2023 07:15:35 +0200
Subject: [PATCH 234/601] adding easyconfigs: NAGfor-7.1.eb

---
 easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb | 30 ++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb

diff --git a/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb b/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb
new file mode 100644
index 00000000000..3560fb4a995
--- /dev/null
+++ b/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb
@@ -0,0 +1,30 @@
+easyblock = 'Binary'
+
+name = 'NAGfor'
+version = '7.1'
+
+homepage = 'http://www.nag.co.uk'
+description = """The checking compiler for improved code portability and detailed error reporting."""
+
+toolchain = SYSTEM
+
+sources = [{
+    'source_urls': ['https://www.nag.co.uk/downloads/impl'],
+    'filename': SOURCE_TGZ,
+    'download_filename': 'npl6a%(version_major)s%(version_minor)sna_amd64.tgz'
+}]
+checksums = ['0f173ea0e0809673db216622a7354cc2eb52bf13372a34ef85e62a115bb6f94f']
+
+extract_sources = True
+
+install_cmd = "INSTALL_TO_BINDIR=%(installdir)s/bin INSTALL_TO_LIBDIR=%(installdir)s/lib "
+install_cmd += "INSTALL_TO_CATMANDIR=%(installdir)s/man INSTALL_TO_MANDIR=%(installdir)s/man ./INSTALLU.sh"
+
+modextravars = {'NAG_KUSARI_FILE': HOME + '/licenses/license.dat'}
+
+sanity_check_paths = {
+    'files': ['bin/dbx90', 'bin/nagfmcheck', 'bin/nagfor'],
+    'dirs': ['lib', 'man1', 'man3'],
+}
+
+moduleclass = 'compiler'

From 85746125490e06419ff2b1fb019c9f8042f5fd65 Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Wed, 5 Apr 2023 07:37:41 +0200
Subject: [PATCH 235/601] adding easyconfigs: NAG-7.1-gompi-2022b.eb

---
 .../easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb  | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb

diff --git a/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb b/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb
new file mode 100644
index 00000000000..dd7e50c3ced
--- /dev/null
+++ b/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb
@@ -0,0 +1,30 @@
+easyblock = 'Binary'
+
+name = 'NAG'
+version = '7.1'
+
+homepage = 'http://www.nag.co.uk'
+description = "The worlds largest collection of robust, documented, tested and maintained numerical algorithms."
+
+toolchain = {'name': 'gompi', 'version': '2022b'}
+
+sources = [{
+    'source_urls': ['https://www.nag.co.uk/downloads/impl'],
+    'filename': SOURCE_TGZ,
+    'download_filename': 'npl6a%(version_major)s%(version_minor)sna_amd64.tgz'
+}]
+checksums = ['0f173ea0e0809673db216622a7354cc2eb52bf13372a34ef85e62a115bb6f94f']
+
+extract_sources = True
+
+install_cmd = "INSTALL_TO_BINDIR=%(installdir)s/bin INSTALL_TO_LIBDIR=%(installdir)s/lib "
+install_cmd += "INSTALL_TO_CATMANDIR=%(installdir)s/man INSTALL_TO_MANDIR=%(installdir)s/man ./INSTALLU.sh"
+
+modextravars = {'NAG_KUSARI_FILE': HOME + '/licenses/license.dat'}
+
+sanity_check_paths = {
+    'files': ['bin/dbx90', 'bin/nagfmcheck', 'bin/nagfor'],
+    'dirs': ['lib', 'man1', 'man3'],
+}
+
+moduleclass = 'compiler'

From 8515aff4fb9772cc21d4e262e8343d780462abfa Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Wed, 5 Apr 2023 08:02:43 +0200
Subject: [PATCH 236/601] adding easyconfigs: argtable-2.13-GCCcore-10.2.0.eb

---
 .../argtable/argtable-2.13-GCCcore-10.2.0.eb  | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb

diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..896c6221885
--- /dev/null
+++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb
@@ -0,0 +1,30 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# Modified by: Adam Huffman
+# The Francis Crick Institute
+
+easyblock = 'ConfigureMake'
+
+name = 'argtable'
+version = '2.13'
+
+homepage = 'http://argtable.sourceforge.net/'
+description = """ Argtable is an ANSI C library for parsing GNU style
+ command line options with a minimum of fuss. """
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))]
+checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf']
+
+builddependencies = [('binutils', '2.35')]
+
+sanity_check_paths = {
+    'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'],
+    'dirs': ['share'],
+}
+
+moduleclass = 'lib'

From 50437f2a1f2dc34c39e051cce1545c6c57e08e7f Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Wed, 5 Apr 2023 08:03:38 +0200
Subject: [PATCH 237/601] adding easyconfigs: Clustal-Omega-1.2.4-GCC-10.2.0.eb

---
 .../Clustal-Omega-1.2.4-GCC-10.2.0.eb         | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb

diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb
new file mode 100644
index 00000000000..df007a1ade5
--- /dev/null
+++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb
@@ -0,0 +1,35 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# Modified by Adam Huffman
+# Francis Crick Institute
+
+easyblock = 'ConfigureMake'
+
+name = 'Clustal-Omega'
+version = '1.2.4'
+
+homepage = 'http://www.clustal.org/omega/'
+description = """ Clustal Omega is a multiple sequence alignment
+ program for proteins. It produces biologically meaningful multiple
+ sequence alignments of divergent sequences. Evolutionary relationships
+ can be seen via viewing Cladograms or Phylograms """
+
+toolchain = {'name': 'GCC', 'version': '10.2.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee']
+
+dependencies = [('argtable', '2.13')]
+
+sanity_check_paths = {
+    'files': ['bin/clustalo'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["clustalo --help"]
+
+moduleclass = 'bio'

From cd4122cb5460428f215d2d76b8f3784ed1069e33 Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Wed, 5 Apr 2023 08:21:02 +0200
Subject: [PATCH 238/601] adding easyconfigs: c-ares-1.17.2-GCCcore-10.2.0.eb

---
 .../c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb  | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb

diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..6b168c49490
--- /dev/null
+++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb
@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'c-ares'
+version = '1.17.2'
+
+homepage = 'https://c-ares.haxx.se'
+description = "c-ares is a C library for asynchronous DNS requests (including name resolves)"
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://c-ares.haxx.se/download/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['4803c844ce20ce510ef0eb83f8ea41fa24ecaae9d280c468c582d2bb25b3913d']
+
+builddependencies = [('binutils', '2.35')]
+
+sanity_check_paths = {
+    'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'],
+    'dirs': ['include', 'share/man'],
+}
+
+moduleclass = 'lib'

From 380e32d184f6777edeb07d41775901bc04adcfed Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Wed, 5 Apr 2023 08:25:20 +0200
Subject: [PATCH 239/601] adding easyconfigs: CppUnit-1.15.1-GCCcore-10.2.0.eb

---
 .../CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb  | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb

diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..61e5d8e491f
--- /dev/null
+++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'CppUnit'
+version = '1.15.1'
+
+homepage = 'https://freedesktop.org/wiki/Software/cppunit/'
+
+description = """
+ CppUnit is the C++ port of the famous JUnit framework for unit testing.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ['https://dev-www.libreoffice.org/src']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7']
+
+builddependencies = [
+    ('binutils', '2.35'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT,
+              'lib/pkgconfig/cppunit.pc'],
+    'dirs': ['bin', 'include/cppunit', 'share'],
+}
+
+moduleclass = 'tools'

From 5591eb1c417170181ea60432b4ee6a539d5a54c6 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Wed, 5 Apr 2023 09:04:02 +0200
Subject: [PATCH 240/601] adding easyconfigs: geopandas-0.12.2-foss-2022b.eb,
 pyproj-3.5.0-GCCcore-12.2.0.eb, Fiona-1.9.2-foss-2022b.eb

---
 .../f/Fiona/Fiona-1.9.2-foss-2022b.eb         | 48 +++++++++++++++++++
 .../geopandas/geopandas-0.12.2-foss-2022b.eb  | 38 +++++++++++++++
 .../p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb   | 37 ++++++++++++++
 3 files changed, 123 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb
new file mode 100644
index 00000000000..024b51efc9f
--- /dev/null
+++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb
@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'Fiona'
+version = '1.9.2'
+
+homepage = 'https://github.com/Toblerity/Fiona'
+description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data
+in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries,
+mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using
+multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS
+packages such as pyproj, Rtree, and Shapely."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('GDAL', '3.6.2'),
+    ('Shapely', '2.0.1'),  # optional for 'calc' extras
+]
+
+use_pip = True
+
+exts_list = [
+    ('cligj', '0.7.2', {
+        'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'],
+    }),
+    ('click-plugins', '1.1.1', {
+        'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'],
+    }),
+    ('munch', '2.5.0', {
+        'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'],
+    }),
+    (name, version, {
+        'use_pip_extras': 'calc',
+        'checksums': ['f9263c5f97206bf2eb2c010d52e8ffc54e96886b0e698badde25ff109b32952a'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/fio'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["fio --help"]
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb
new file mode 100644
index 00000000000..a887dfe6e14
--- /dev/null
+++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'geopandas'
+version = '0.12.2'
+
+homepage = 'https://github.com/geopandas/geopandas'
+description = """GeoPandas is a project to add support for geographic data to pandas objects.
+It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series
+and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and
+perform geometric operations."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('Shapely', '2.0.1'),
+    ('Fiona', '1.9.2'),
+    ('matplotlib', '3.7.0'),
+    ('pyproj', '3.5.0'),
+    ('networkx', '3.0'),  # needed by mapclassify
+    ('scikit-learn', '1.2.1'),  # needed by mapclassify
+]
+
+use_pip = True
+
+exts_list = [
+    ('mapclassify', '2.4.3', {
+        'checksums': ['51b81e1f1ee7f64a4ca1e9f61f01216c364a3f086a48b1be38eb057199cb19bf'],
+    }),
+    (name, version, {
+        'checksums': ['0acdacddefa176525e4da6d9aeeece225da26055c4becdc6e97cf40fa97c27f4'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'geo'
diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..f90f4e9a5b1
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonPackage'
+
+name = 'pyproj'
+version = '3.5.0'
+
+homepage = 'https://pyproj4.github.io/pyproj'
+description = "Python interface to PROJ4 library for cartographic transformations"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['9859d1591c1863414d875ae0759e72c2cffc01ab989dc64137fbac572cc81bf6']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('PROJ', '9.1.1'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+preinstallopts = "export PROJ_DIR=$EBROOTPROJ && "
+
+sanity_check_paths = {
+    'files': ['bin/pyproj'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['pyproj --help']
+
+sanity_pip_check = True
+
+moduleclass = 'data'

From 3dcc9283930533263247488ff2141674c7a252f7 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 5 Apr 2023 09:49:24 +0200
Subject: [PATCH 241/601] add missing dependency on wget to FunGAP v1.1.1

---
 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
index a974e867d2b..f2205d273fb 100644
--- a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb
@@ -49,6 +49,7 @@ dependencies = [
     ('SAMtools', '1.16.1'),
     ('SNAP-HMM', '20221022'),
     ('Trinity', '2.15.1'),
+    ('wget', '1.21.3'),
 ]
 
 exts_defaultclass = 'PythonPackage'

From 88e912c866965ce0ec5ddbda38a68df7bb003cee Mon Sep 17 00:00:00 2001
From: ll4strw <lenocil@strw.leidenuniv.nl>
Date: Wed, 5 Apr 2023 10:31:34 +0200
Subject: [PATCH 242/601] Using SYSTEM toolchain

---
 .../{cppzmq-4.9.0-GCC-11.2.0.eb => cppzmq-4.9.0.eb}    | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)
 rename easybuild/easyconfigs/c/cppzmq/{cppzmq-4.9.0-GCC-11.2.0.eb => cppzmq-4.9.0.eb} (67%)

diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb
similarity index 67%
rename from easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb
rename to easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb
index e78d4d15a99..0f78f6e8ed9 100644
--- a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb
@@ -1,3 +1,4 @@
+# ll4strw Lorentz Institute
 easyblock = 'CMakeMake'
 
 name = 'cppzmq'
@@ -6,17 +7,20 @@ version = '4.9.0'
 homepage = 'https://github.com/zeromq/cppzmq'
 description = "cppzmq is a C++ binding for libzmq."
 
-toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchain = SYSTEM
 
 source_urls = ['https://github.com/zeromq/%(name)s/archive/refs/tags/']
 sources = ['v%(version)s.tar.gz']
 checksums = ['3fdf5b100206953f674c94d40599bdb3ea255244dcc42fab0d75855ee3645581']
 
 builddependencies = [
-    ('CMake', '3.22.1'),
-    ('ZeroMQ', '4.3.4'),
+    ('binutils', '2.37', '', ('GCCcore', '11.2.0')),
+    ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')),
+    ('ZeroMQ', '4.3.4', '', ('GCCcore', '11.2.0')),
 ]
 
+separate_build_dir = True
+
 sanity_check_paths = {
     'files': ['include/zmq.hpp'],
     'dirs': ['include', 'lib'],

From 8621a5a87da6b5771d1bc456fd526624c2e6b49b Mon Sep 17 00:00:00 2001
From: anselmicz <jakubkropacek@email.cz>
Date: Wed, 5 Apr 2023 11:38:24 +0200
Subject: [PATCH 243/601] Add Autotools to builddependencies

---
 easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
index 45c70aeb5f0..2b6f884979c 100644
--- a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
@@ -18,6 +18,7 @@ checksums = ['e8ee79b1f399b2d167e6a90de52ccc90e52408f7ade1b9b7135727efe181347f']
 builddependencies = [
     ('binutils', '2.39'),
     ('pkgconf', '1.9.3'),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [

From f9393a8ad3fee6369e40103b6eaa8045dfe99e60 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?=
 <77022965+anselmicz@users.noreply.github.com>
Date: Wed, 5 Apr 2023 12:10:06 +0200
Subject: [PATCH 244/601] Update sysbench-1.0.20-GCC-12.2.0.eb

---
 easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
index 2b6f884979c..8634f5e8d18 100644
--- a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb
@@ -16,9 +16,9 @@ sources = ['%(version)s.tar.gz']
 checksums = ['e8ee79b1f399b2d167e6a90de52ccc90e52408f7ade1b9b7135727efe181347f']
 
 builddependencies = [
+    ('Autotools', '20220317'),
     ('binutils', '2.39'),
     ('pkgconf', '1.9.3'),
-    ('Autotools', '20220317'),
 ]
 
 dependencies = [

From e33679eca19da9f396e22e73c7c53fe6af7067a7 Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Wed, 5 Apr 2023 13:15:22 +0200
Subject: [PATCH 245/601] adding easyconfigs: unicore-uftp-1.4.2-Java-1.8.eb

---
 .../unicore-uftp-1.4.2-Java-1.8.eb            | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb

diff --git a/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb
new file mode 100644
index 00000000000..cc641945cc6
--- /dev/null
+++ b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb
@@ -0,0 +1,28 @@
+easyblock = 'PackedBinary'
+
+name = 'unicore-uftp'
+version = '1.4.2'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://sourceforge.net/projects/unicore/'
+description = """UNICORE Java-based client for UFTP"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://downloads.sourceforge.net/project/unicore/Clients/UFTP-Client/%(version)s']
+sources = ['uftp-client-%(version)s-all.zip']
+checksums = ['49670714416077274a0dfdc261e5552bcabbdd5cc4454181a794158491524c54']
+
+# specify dependency on Java/1.8 "wrapper", rather than a specific Java version
+dependencies = [('Java', '1.8', '', True)]
+
+postinstallcmds = ["chmod +x %(installdir)s/bin/uftp"]
+
+sanity_check_paths = {
+    'files': ['bin/uftp'],
+    'dirs': ['bin', 'lib'],
+}
+
+sanity_check_commands = [('uftp', '-version')]
+
+moduleclass = 'tools'

From 9b79d406df113d4d746b364bedc32c99ab40f035 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 5 Apr 2023 13:25:25 +0200
Subject: [PATCH 246/601] New Longshot using Cargo easyblock

---
 .../Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb | 319 +++++++++++++++++-
 1 file changed, 306 insertions(+), 13 deletions(-)

diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb
index d1e9278c0bf..d24ee4f3b3c 100644
--- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb
@@ -1,8 +1,4 @@
-# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
-# Updated to 0.4.3 and GCCcore-10.2.0
-# J. Sassmannshausen (GSTT/NHS UK)
-#
-easyblock = 'Binary'
+easyblock = 'Cargo'
 
 name = 'Longshot'
 version = '0.4.5'
@@ -15,26 +11,323 @@ description = """Longshot is a variant calling tool for diploid genomes using lo
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-github_account = 'pjedge'
-source_urls = [GITHUB_SOURCE]
+crates = [
+    ('addr2line', '0.19.0'),
+    ('adler', '1.0.2'),
+    ('ahash', '0.7.6'),
+    ('aho-corasick', '0.7.20'),
+    ('android_system_properties', '0.1.5'),
+    ('ansi_term', '0.12.1'),
+    ('approx', '0.3.2'),
+    ('atty', '0.2.14'),
+    ('autocfg', '1.1.0'),
+    ('backtrace', '0.3.67'),
+    ('bio', '0.25.0'),
+    ('bio-types', '0.13.0'),
+    ('bit-set', '0.5.3'),
+    ('bit-vec', '0.6.3'),
+    ('bitflags', '1.3.2'),
+    ('bumpalo', '3.12.0'),
+    ('bv', '0.10.0'),
+    ('bytecount', '0.3.2'),
+    ('byteorder', '1.4.3'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cc', '1.0.79'),
+    ('cfg-if', '1.0.0'),
+    ('chrono', '0.4.24'),
+    ('clap', '2.34.0'),
+    ('cmake', '0.1.50'),
+    ('codespan-reporting', '0.11.1'),
+    ('core-foundation-sys', '0.8.3'),
+    ('csv', '1.2.1'),
+    ('csv-core', '0.1.10'),
+    ('curl-sys', '0.4.61+curl-8.0.1'),
+    ('custom_derive', '0.1.7'),
+    ('cxx', '1.0.94'),
+    ('cxx-build', '1.0.94'),
+    ('cxxbridge-flags', '1.0.94'),
+    ('cxxbridge-macro', '1.0.94'),
+    ('derive-new', '0.5.9'),
+    ('either', '1.8.1'),
+    ('error-chain', '0.12.4'),
+    ('feature-probe', '0.1.1'),
+    ('fishers_exact', '1.0.1'),
+    ('fnv', '1.0.7'),
+    ('form_urlencoded', '1.1.0'),
+    ('fs-utils', '1.1.4'),
+    ('fuchsia-cprng', '0.1.1'),
+    ('fxhash', '0.2.1'),
+    ('getrandom', '0.2.8'),
+    ('gimli', '0.27.2'),
+    ('glob', '0.3.1'),
+    ('hashbrown', '0.11.2'),
+    ('heck', '0.4.1'),
+    ('hermit-abi', '0.1.19'),
+    ('hts-sys', '2.0.3'),
+    ('iana-time-zone', '0.1.54'),
+    ('iana-time-zone-haiku', '0.1.1'),
+    ('idna', '0.3.0'),
+    ('ieee754', '0.2.6'),
+    ('itertools', '0.7.11'),
+    ('itertools-num', '0.1.3'),
+    ('itoa', '1.0.6'),
+    ('jobserver', '0.1.26'),
+    ('js-sys', '0.3.61'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.140'),
+    ('libz-sys', '1.1.8'),
+    ('linear-map', '1.2.0'),
+    ('link-cplusplus', '1.0.8'),
+    ('log', '0.4.17'),
+    ('lzma-sys', '0.1.20'),
+    ('matrixmultiply', '0.1.15'),
+    ('memchr', '2.5.0'),
+    ('miniz_oxide', '0.6.2'),
+    ('multimap', '0.4.0'),
+    ('ndarray', '0.12.1'),
+    ('newtype_derive', '0.1.6'),
+    ('num-complex', '0.2.4'),
+    ('num-integer', '0.1.45'),
+    ('num-traits', '0.2.15'),
+    ('object', '0.30.3'),
+    ('once_cell', '1.17.1'),
+    ('openssl-src', '111.25.2+1.1.1t'),
+    ('openssl-sys', '0.9.83'),
+    ('ordered-float', '1.1.1'),
+    ('percent-encoding', '2.2.0'),
+    ('pkg-config', '0.3.26'),
+    ('ppv-lite86', '0.2.17'),
+    ('proc-macro2', '1.0.54'),
+    ('quick-error', '1.2.3'),
+    ('quote', '1.0.26'),
+    ('rand', '0.3.23'),
+    ('rand', '0.4.6'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.3.1'),
+    ('rand_core', '0.4.2'),
+    ('rand_core', '0.6.4'),
+    ('rawpointer', '0.1.0'),
+    ('rdrand', '0.4.0'),
+    ('regex', '1.7.3'),
+    ('regex-syntax', '0.6.29'),
+    ('rust-htslib', '0.38.2'),
+    ('rustc-demangle', '0.1.22'),
+    ('rustc_version', '0.1.7'),
+    ('rustversion', '1.0.12'),
+    ('ryu', '1.0.13'),
+    ('scratch', '1.0.5'),
+    ('semver', '0.1.20'),
+    ('serde', '1.0.159'),
+    ('serde_derive', '1.0.159'),
+    ('statrs', '0.9.0'),
+    ('strsim', '0.8.0'),
+    ('strum_macros', '0.24.3'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.12'),
+    ('termcolor', '1.2.0'),
+    ('textwrap', '0.11.0'),
+    ('thiserror', '1.0.40'),
+    ('thiserror-impl', '1.0.40'),
+    ('time', '0.1.45'),
+    ('tinyvec', '1.6.0'),
+    ('tinyvec_macros', '0.1.1'),
+    ('unicode-bidi', '0.3.13'),
+    ('unicode-ident', '1.0.8'),
+    ('unicode-normalization', '0.1.22'),
+    ('unicode-width', '0.1.10'),
+    ('url', '2.3.1'),
+    ('vcpkg', '0.2.15'),
+    ('vec_map', '0.8.2'),
+    ('version_check', '0.9.4'),
+    ('wasi', '0.10.0+wasi-snapshot-preview1'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('wasm-bindgen', '0.2.84'),
+    ('wasm-bindgen-backend', '0.2.84'),
+    ('wasm-bindgen-macro', '0.2.84'),
+    ('wasm-bindgen-macro-support', '0.2.84'),
+    ('wasm-bindgen-shared', '0.2.84'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.5'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows', '0.46.0'),
+    ('windows-targets', '0.42.2'),
+    ('windows_aarch64_gnullvm', '0.42.2'),
+    ('windows_aarch64_msvc', '0.42.2'),
+    ('windows_i686_gnu', '0.42.2'),
+    ('windows_i686_msvc', '0.42.2'),
+    ('windows_x86_64_gnu', '0.42.2'),
+    ('windows_x86_64_gnullvm', '0.42.2'),
+    ('windows_x86_64_msvc', '0.42.2'),
+]
+source_urls = ['https://github.com/pjedge/longshot/archive']
 sources = ['v%(version)s.tar.gz']
-checksums = ['7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad']
+checksums = [
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+    {'v0.4.5.tar.gz': '7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad'},
+    {'addr2line-0.19.0.tar.gz': 'a76fd60b23679b7d19bd066031410fb7e458ccc5e958eb5c325888ce4baedc97'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'},
+    {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'},
+    {'android_system_properties-0.1.5.tar.gz': '819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311'},
+    {'ansi_term-0.12.1.tar.gz': 'd52a9bb7ec0cf484c551830a7ce27bd20d67eac647e1befb56b0be4ee39a55d2'},
+    {'approx-0.3.2.tar.gz': 'f0e60b75072ecd4168020818c0107f2857bb6c4e64252d8d3983f6263b40a5c3'},
+    {'atty-0.2.14.tar.gz': 'd9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8'},
+    {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'},
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+    {'clap-2.34.0.tar.gz': 'a0610544180c38b88101fecf2dd634b174a62eef6946f84dfc6a7127512b381c'},
+    {'cmake-0.1.50.tar.gz': 'a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130'},
+    {'codespan-reporting-0.11.1.tar.gz': '3538270d33cc669650c4b093848450d380def10c331d38c768e34cac80576e6e'},
+    {'core-foundation-sys-0.8.3.tar.gz': '5827cebf4670468b8772dd191856768aedcb1b0278a04f989f7766351917b9dc'},
+    {'csv-1.2.1.tar.gz': '0b015497079b9a9d69c02ad25de6c0a6edef051ea6360a327d0bd05802ef64ad'},
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+    {'cxx-1.0.94.tar.gz': 'f61f1b6389c3fe1c316bf8a4dccc90a38208354b330925bce1f74a6c4756eb93'},
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+    {'cxxbridge-flags-1.0.94.tar.gz': '7944172ae7e4068c533afbb984114a56c46e9ccddda550499caa222902c7f7bb'},
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+    {'either-1.8.1.tar.gz': '7fcaabb2fef8c910e7f4c7ce9f67a1283a1715879a7c230ca9d6d1ae31f16d91'},
+    {'error-chain-0.12.4.tar.gz': '2d2f06b9cac1506ece98fe3231e3cc9c4410ec3d5b1f24ae1c8946f0742cdefc'},
+    {'feature-probe-0.1.1.tar.gz': '835a3dc7d1ec9e75e2b5fb4ba75396837112d2060b03f7d43bc1897c7f7211da'},
+    {'fishers_exact-1.0.1.tar.gz': '64993467e77edcbfce160dae38337b4c538aa0e8027039c6eabba8fa335c7b1e'},
+    {'fnv-1.0.7.tar.gz': '3f9eec918d3f24069decb9af1554cad7c880e2da24a9afd88aca000531ab82c1'},
+    {'form_urlencoded-1.1.0.tar.gz': 'a9c384f161156f5260c24a097c56119f9be8c798586aecc13afbcbe7b7e26bf8'},
+    {'fs-utils-1.1.4.tar.gz': '6fc7a9dc005c944c98a935e7fd626faf5bf7e5a609f94bc13e42fc4a02e52593'},
+    {'fuchsia-cprng-0.1.1.tar.gz': 'a06f77d526c1a601b7c4cdd98f54b5eaabffc14d5f2f0296febdc7f357c6d3ba'},
+    {'fxhash-0.2.1.tar.gz': 'c31b6d751ae2c7f11320402d34e41349dd1016f8d5d45e48c4312bc8625af50c'},
+    {'getrandom-0.2.8.tar.gz': 'c05aeb6a22b8f62540c194aac980f2115af067bfe15a0734d7277a768d396b31'},
+    {'gimli-0.27.2.tar.gz': 'ad0a93d233ebf96623465aad4046a8d3aa4da22d4f4beba5388838c8a434bbb4'},
+    {'glob-0.3.1.tar.gz': 'd2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b'},
+    {'hashbrown-0.11.2.tar.gz': 'ab5ef0d4909ef3724cc8cce6ccc8572c5c817592e9285f5464f8e86f8bd3726e'},
+    {'heck-0.4.1.tar.gz': '95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8'},
+    {'hermit-abi-0.1.19.tar.gz': '62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33'},
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+    {'idna-0.3.0.tar.gz': 'e14ddfc70884202db2244c223200c204c2bda1bc6e0998d11b5e024d657209e6'},
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+    {'miniz_oxide-0.6.2.tar.gz': 'b275950c28b37e794e8c55d88aeb5e139d0ce23fdbbeda68f8d7174abdf9e8fa'},
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+    {'ordered-float-1.1.1.tar.gz': '3305af35278dd29f46fcdd139e0b1fbfae2153f0e5928b39b035542dd31e37b7'},
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+    {'pkg-config-0.3.26.tar.gz': '6ac9a59f73473f1b8d852421e59e64809f025994837ef743615c6d0c5b305160'},
+    {'ppv-lite86-0.2.17.tar.gz': '5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de'},
+    {'proc-macro2-1.0.54.tar.gz': 'e472a104799c74b514a57226160104aa483546de37e839ec50e3c2e41dd87534'},
+    {'quick-error-1.2.3.tar.gz': 'a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0'},
+    {'quote-1.0.26.tar.gz': '4424af4bf778aae2051a77b60283332f386554255d722233d09fbfc7e30da2fc'},
+    {'rand-0.3.23.tar.gz': '64ac302d8f83c0c1974bf758f6b041c6c8ada916fbb44a609158ca8b064cc76c'},
+    {'rand-0.4.6.tar.gz': '552840b97013b1a26992c11eac34bdd778e464601a4c2054b5f0bff7c6761293'},
+    {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'},
+    {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'},
+    {'rand_core-0.3.1.tar.gz': '7a6fdeb83b075e8266dcc8762c22776f6877a63111121f5f8c7411e5be7eed4b'},
+    {'rand_core-0.4.2.tar.gz': '9c33a3c44ca05fa6f1807d8e6743f3824e8509beca625669633be0acbdf509dc'},
+    {'rand_core-0.6.4.tar.gz': 'ec0be4795e2f6a28069bec0b5ff3e2ac9bafc99e6a9a7dc3547996c5c816922c'},
+    {'rawpointer-0.1.0.tar.gz': 'ebac11a9d2e11f2af219b8b8d833b76b1ea0e054aa0e8d8e9e4cbde353bdf019'},
+    {'rdrand-0.4.0.tar.gz': '678054eb77286b51581ba43620cc911abf02758c91f93f479767aed0f90458b2'},
+    {'regex-1.7.3.tar.gz': '8b1f693b24f6ac912f4893ef08244d70b6067480d2f1a46e950c9691e6749d1d'},
+    {'regex-syntax-0.6.29.tar.gz': 'f162c6dd7b008981e4d40210aca20b4bd0f9b60ca9271061b07f78537722f2e1'},
+    {'rust-htslib-0.38.2.tar.gz': '2aca6626496389f6e015e25433b85e2895ad3644b44de91167d847bf2d8c1a1c'},
+    {'rustc-demangle-0.1.22.tar.gz': 'd4a36c42d1873f9a77c53bde094f9664d9891bc604a45b4798fd2c389ed12e5b'},
+    {'rustc_version-0.1.7.tar.gz': 'c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084'},
+    {'rustversion-1.0.12.tar.gz': '4f3208ce4d8448b3f3e7d168a73f5e0c43a61e32930de3bceeccedb388b6bf06'},
+    {'ryu-1.0.13.tar.gz': 'f91339c0467de62360649f8d3e185ca8de4224ff281f66000de5eb2a77a79041'},
+    {'scratch-1.0.5.tar.gz': '1792db035ce95be60c3f8853017b3999209281c24e2ba5bc8e59bf97a0c590c1'},
+    {'semver-0.1.20.tar.gz': 'd4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac'},
+    {'serde-1.0.159.tar.gz': '3c04e8343c3daeec41f58990b9d77068df31209f2af111e059e9fe9646693065'},
+    {'serde_derive-1.0.159.tar.gz': '4c614d17805b093df4b147b51339e7e44bf05ef59fba1e45d83500bcfb4d8585'},
+    {'statrs-0.9.0.tar.gz': '7d8c8660e3867d1a0578cbf7fd9532f1368b7460bd00b080e2d4669618a9bec7'},
+    {'strsim-0.8.0.tar.gz': '8ea5119cdb4c55b55d432abb513a0429384878c15dde60cc77b1c99de1a95a6a'},
+    {'strum_macros-0.24.3.tar.gz': '1e385be0d24f186b4ce2f9982191e7101bb737312ad61c1f2f984f34bcf85d59'},
+    {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'},
+    {'syn-2.0.12.tar.gz': '79d9531f94112cfc3e4c8f5f02cb2b58f72c97b7efd85f70203cc6d8efda5927'},
+    {'termcolor-1.2.0.tar.gz': 'be55cf8942feac5c765c2c993422806843c9a9a45d4d5c407ad6dd2ea95eb9b6'},
+    {'textwrap-0.11.0.tar.gz': 'd326610f408c7a4eb6f51c37c330e496b08506c9457c9d34287ecc38809fb060'},
+    {'thiserror-1.0.40.tar.gz': '978c9a314bd8dc99be594bc3c175faaa9794be04a5a5e153caba6915336cebac'},
+    {'thiserror-impl-1.0.40.tar.gz': 'f9456a42c5b0d803c8cd86e73dd7cc9edd429499f37a3550d286d5e86720569f'},
+    {'time-0.1.45.tar.gz': '1b797afad3f312d1c66a56d11d0316f916356d11bd158fbc6ca6389ff6bf805a'},
+    {'tinyvec-1.6.0.tar.gz': '87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50'},
+    {'tinyvec_macros-0.1.1.tar.gz': '1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20'},
+    {'unicode-bidi-0.3.13.tar.gz': '92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460'},
+    {'unicode-ident-1.0.8.tar.gz': 'e5464a87b239f13a63a501f2701565754bae92d243d4bb7eb12f6d57d2269bf4'},
+    {'unicode-normalization-0.1.22.tar.gz': '5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921'},
+    {'unicode-width-0.1.10.tar.gz': 'c0edd1e5b14653f783770bce4a4dabb4a5108a5370a5f5d8cfe8710c361f6c8b'},
+    {'url-2.3.1.tar.gz': '0d68c799ae75762b8c3fe375feb6600ef5602c883c5d21eb51c09f22b83c4643'},
+    {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'},
+    {'vec_map-0.8.2.tar.gz': 'f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191'},
+    {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'},
+    {'wasi-0.10.0+wasi-snapshot-preview1.tar.gz': '1a143597ca7c7793eff794def352d41792a93c481eb1042423ff7ff72ba2c31f'},
+    {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'},
+    {'wasm-bindgen-0.2.84.tar.gz': '31f8dcbc21f30d9b8f2ea926ecb58f6b91192c17e9d33594b3df58b2007ca53b'},
+    {'wasm-bindgen-backend-0.2.84.tar.gz': '95ce90fd5bcc06af55a641a86428ee4229e44e07033963a2290a8e241607ccb9'},
+    {'wasm-bindgen-macro-0.2.84.tar.gz': '4c21f77c0bedc37fd5dc21f897894a5ca01e7bb159884559461862ae90c0b4c5'},
+    {'wasm-bindgen-macro-support-0.2.84.tar.gz': '2aff81306fcac3c7515ad4e177f521b5c9a15f2b08f4e32d823066102f35a5f6'},
+    {'wasm-bindgen-shared-0.2.84.tar.gz': '0046fef7e28c3804e5e38bfa31ea2a0f73905319b677e57ebe37e49358989b5d'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'windows-0.46.0.tar.gz': 'cdacb41e6a96a052c6cb63a144f24900236121c6f63f4f8219fef5977ecb0c25'},
+    {'windows-targets-0.42.2.tar.gz': '8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'},
+    {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'},
+    {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'},
+    {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'},
+    {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'},
+    {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'},
+    {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'},
+    {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'},
+]
 
 builddependencies = [
     ('binutils', '2.38'),
     ('Rust', '1.65.0'),
     ('Clang', '13.0.1'),
-    ('CMake', '3.23.1'),
+    ('Perl', '5.34.1'),
+    ('CMake', '3.24.3'),
 ]
 
 dependencies = [
     ('bzip2', '1.0.8'),
 ]
 
-extract_sources = True
-
-install_cmd = "cargo install --root %(installdir)s --path ."
-
 sanity_check_paths = {
     'files': ['bin/%(namelower)s'],
     'dirs': [],

From 714b5cb02c4cbfdc23ecf98ccf268e8699788db4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?=
 <77022965+anselmicz@users.noreply.github.com>
Date: Wed, 5 Apr 2023 14:00:36 +0200
Subject: [PATCH 247/601] Add libsystemd-dev and systemd-devel as OS
 dependencies

---
 easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
index 1d50e1ff0c1..b6e1bf489ae 100644
--- a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
@@ -23,6 +23,8 @@ dependencies = [
     ('libdrm', '2.4.114'),
 ]
 
+osdependencies = [('libsystemd-dev', 'systemd-devel')]
+
 separate_build_dir = True
 
 sanity_check_paths = {

From d7c96f8050af74e8158c9197e97502c4ca4d3480 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?=
 <77022965+anselmicz@users.noreply.github.com>
Date: Wed, 5 Apr 2023 14:10:55 +0200
Subject: [PATCH 248/601] Add libudev-dev OS dependecy for compatibility with
 Ubuntu 18.04

---
 easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
index b6e1bf489ae..c4dd3f56af6 100644
--- a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb
@@ -23,7 +23,7 @@ dependencies = [
     ('libdrm', '2.4.114'),
 ]
 
-osdependencies = [('libsystemd-dev', 'systemd-devel')]
+osdependencies = [('libsystemd-dev', 'libudev-dev', 'systemd-devel')]
 
 separate_build_dir = True
 

From d704176b57465f43e0a9ec22f4885fe2f13f9a63 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 5 Apr 2023 19:05:50 +0200
Subject: [PATCH 249/601] adding easyconfigs: R-MXM-1.5.5-foss-2021b.eb

---
 .../r/R-MXM/R-MXM-1.5.5-foss-2021b.eb         | 54 +++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb

diff --git a/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb b/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb
new file mode 100644
index 00000000000..fbbc6f6be34
--- /dev/null
+++ b/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb
@@ -0,0 +1,54 @@
+easyblock = 'Bundle'
+
+name = 'R-MXM'
+version = '1.5.5'
+
+homepage = 'https://cran.r-project.org/package=MXM'
+description = "MXM: Feature Selection (Including Multiple Solutions) and Bayesian Networks"
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+dependencies = [
+    ('R', '4.1.2'),
+]
+
+exts_default_options = {
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz'
+}
+
+exts_defaultclass = 'RPackage'
+exts_filter = ("R -q --no-save", "library(%(ext_name)s)")
+
+exts_list = [
+    ('sets', '1.0-24', {
+        'checksums': ['e75733f5c9418eb09fb950a4a94ccf84ddd88231c61ee80d02b7f0917debcac9'],
+    }),
+    ('relations', '0.6-13', {
+        'checksums': ['f859c336fb0c4a2df7f294b33d1d04f95c6988e5e76933e2e70bf291d904d9da'],
+    }),
+    ('RcppZiggurat', '0.1.6', {
+        'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'],
+    }),
+    ('Rfast', '2.0.7', {
+        'checksums': ['8f86159a4760a7124e1c91ae0b022c7e496f81590ea4e4af702bea44e8dedf8f'],
+    }),
+    ('Rfast2', '0.1.4', {
+        'checksums': ['494b777a86342aae0a6a5f0eb189337b846ef2929964672c0f010d93699d0d63'],
+    }),
+    ('MXM', version, {
+        'checksums': ['943d7d3ff8496bad43329614922795b0777fa0787fdfd98f71d90a1a9c952497'],
+    }),
+]
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['MXM'],
+}
+
+moduleclass = 'math'

From 8a0a3f6ac9489d5296711320b746ca7426fb055a Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Thu, 6 Apr 2023 15:33:08 +0200
Subject: [PATCH 250/601] add Compress-Raw-Zlib dep

---
 .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb
index 1f52ef21a7d..7e0b6557ddd 100644
--- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb
@@ -17,6 +17,7 @@ dependencies = [
     ('Jellyfish', '2.3.0'),
     ('Perl', '5.34.1'),
     ('bzip2', '1.0.8'),
+    ('Compress-Raw-Zlib', '2.202'),
 ]
 
 extract_sources = True

From 219658ccea7912568645a4c92490a16ff8d82ae9 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Thu, 6 Apr 2023 15:57:06 +0200
Subject: [PATCH 251/601] add sanity_check_commands

---
 easybuild/easyconfigs/z/zsh/zsh-5.9.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
index ff8bd3f2190..5c8ea48d53c 100644
--- a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
+++ b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb
@@ -25,6 +25,8 @@ sanity_check_paths = {
     'dirs': ['lib/zsh/%(version)s', 'share'],
 }
 
+sanity_check_commands = ['zsh --version']
+
 # optionally make this module sticky (lmod only):
 # modluafooter = 'add_property("lmod", "sticky")'
 

From 9dcfc5b6df98b20b68b7be355724697595ac0082 Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Thu, 6 Apr 2023 16:27:48 +0000
Subject: [PATCH 252/601] adding easyconfigs:
 Seurat-4.3.0-foss-2022a-R-4.2.1.eb

---
 .../Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb | 72 +++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..3529ca55994
--- /dev/null
+++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,72 @@
+easyblock = 'Bundle'
+
+name = 'Seurat'
+version = '4.3.0'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://satijalab.org/seurat'
+description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+    'https://cran.r-project.org/src/contrib/',  # current version of packages
+    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+]
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('R-bundle-Bioconductor', '3.15', versionsuffix),
+]
+
+exts_defaultclass = 'RPackage'
+exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']}
+
+exts_list = [
+    ('Matrix', '1.5-4', {
+        'checksums': ['15ceb61993d61b442068104abb46e6d91b5a1179c01eeb64563b853abab66f06'],
+    }),
+    ('sp', '1.5-1', {
+        'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'],
+    }),
+    ('SeuratObject', '4.1.3', {
+        'checksums': ['585d2754f6165a367f0f458523f0a25d4d4160c929c931b27c5603cc6bd986d3'],
+    }),
+    ('sctransform', '0.3.5', {
+        'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'],
+    }),
+    ('uwot', '0.1.14', {
+        'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'],
+    }),
+    ('spatstat.utils', '3.0-1', {
+        'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'],
+    }),
+    ('spatstat.data', '3.0-0', {
+        'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'],
+    }),
+    ('spatstat.geom', '3.0-3', {
+        'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'],
+    }),
+    ('spatstat.random', '3.0-1', {
+        'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'],
+    }),
+    ('spatstat.sparse', '3.0-0', {
+        'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'],
+    }),
+    ('spatstat.explore', '3.0-5', {
+        'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'],
+    }),
+    (name, version, {
+        'checksums': ['7ebacb3b86f74279de60b597f9a6e728f0668719811b0dca3425d21762fff97c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'bio'

From e5c0fa47b5d50da70b23e6b73c2f07c3bc76403a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Apr 2023 11:38:15 +0200
Subject: [PATCH 253/601] adding easyconfigs: bwa-meth-0.2.6-GCC-11.3.0.eb

---
 .../b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb   | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb
new file mode 100644
index 00000000000..238b5bbcf7b
--- /dev/null
+++ b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb
@@ -0,0 +1,50 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'PythonBundle'
+
+name = 'bwa-meth'
+version = '0.2.6'
+
+homepage = 'https://github.com/brentp/bwa-meth'
+description = """Fast and accurante alignment of BS-Seq reads."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SAMtools', '1.13'),
+    ('BWA', '0.7.17'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('toolshed', '0.4.6', {
+        'checksums': ['23a31c177bf84244b30a9f12c7a8a17a66a2d63043ead0460c31b9ff42f9fb93'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/brentp/bwa-meth/archive'],
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'checksums': ['c1d98aa6d34f103752de7ff3148c9586e5571417accb4a39f5bac8546dab497d'],
+        # fix TypeError when using --help, see https://github.com/brentp/bwa-meth/pull/87
+        'preinstallopts': "sed -i 's/44% /44%% /g' bwameth.py && ",
+        'modulename': 'bwameth',
+    }),
+]
+
+fix_python_shebang_for = ['bin/bwameth.py', 'bin/toolshed']
+
+sanity_check_paths = {
+    'files': ['bin/bwameth.py', 'bin/toolshed'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "toolshed --help",
+    "bwameth.py --help",
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 90ac6ef33c398fd9a210e9e58fe009e2eb9b3520 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 7 Apr 2023 22:59:29 +0200
Subject: [PATCH 254/601] adding easyconfigs: SMAP-4.6.5-foss-2022a.eb and
 patches: SMAP-4.6.5_no-bin-bedtools.patch

---
 .../s/SMAP/SMAP-4.6.5-foss-2022a.eb           | 80 +++++++++++++++++++
 .../s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch   | 15 ++++
 2 files changed, 95 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch

diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb
new file mode 100644
index 00000000000..ecf81cc47c8
--- /dev/null
+++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb
@@ -0,0 +1,80 @@
+easyblock = 'PythonBundle'
+
+name = 'SMAP'
+version = '4.6.5'
+
+homepage = 'https://ngs-smap.readthedocs.io'
+description = "SMAP is an analysis tool for stack-based NGS read mapping"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),  # for pandas
+    ('matplotlib', '3.5.2'),
+    ('BEDTools', '2.30.0'),
+    ('pybedtools', '0.9.0'),
+    ('Pysam', '0.19.1'),
+    ('Biopython', '1.79'),
+    ('openpyxl', '3.0.10'),
+    ('plotly.py', '5.12.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('setuptools', '67.6.1', {
+        'checksums': ['257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a'],
+    }),
+    ('colorlog', '6.7.0', {
+        'checksums': ['bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5'],
+    }),
+    ('primer3-py', '1.2.0', {
+        'checksums': ['9e511e90987d4beda11f1f065b81805bc0c26a08084154e87fda46136ecf7518'],
+        'modulename': 'primer3',
+    }),
+    ('dnaio', '0.10.0', {
+        'checksums': ['de51a50948f00b864297d74eddb588fbee5ac229855754e77564d18b24619d18'],
+    }),
+    ('isal', '1.1.0', {
+        'checksums': ['1364f4e3255a57d51c01422ab3ae785a43c076d516ebf49f6a25adecf8232105'],
+    }),
+    ('xopen', '1.7.0', {
+        'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'],
+    }),
+    # smap-haplotype-window 1.8.1 requires cutadapt <= 4.1 (requires cutadapt.utils.reverse_complemented_sequence)
+    ('cutadapt', '4.1', {
+        'checksums': ['be745ff24adfb4a3eaf715dfad0e2ccdfad7792ef00c1122adf4fbf3aed9227b'],
+    }),
+    ('ngs-smap', version, {
+        'patches': ['SMAP-4.6.5_no-bin-bedtools.patch'],
+        'checksums': [
+            {'ngs-smap-4.6.5.tar.gz': 'bd6fd5a9fb5be66c5d21410376ed6b13eeb23da040c498d60dad6a8fb45d9d5e'},
+            {'SMAP-4.6.5_no-bin-bedtools.patch': 'a43460694378628129d2cd3373e850fccb2ca330680f6fea3e31db9e4589d7ca'},
+        ],
+        'preinstallopts': "rm bin/bedtools && sed -i 's/~=/>=/g' setup.cfg && ",
+        'modulename': 'smap',
+    }),
+    ('smap-haplotype-window', '1.8.1', {
+        'checksums': ['5e244ecec8cb798d294014378c735dd2ab3d32f8266c7d161cf733099715fbbe'],
+        'modulename': 'smap_window',
+    }),
+    ('gffpandas', '1.2.0', {
+        'checksums': ['1a1e1c5c5120bf46ec57517222ebb42ffaab3f768c972fec54c4ac1b07b7f0c6'],
+    }),
+    ('smap-effect-prediction', '0.1.2', {
+        'checksums': ['af16135eb3a2d9c22287a06d595010c46957711358734d73daaa21059ac27ca2'],
+        'preinstallopts': "sed -i 's/~=/>=/g' setup.cfg && ",
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/smap'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["smap compare --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch
new file mode 100644
index 00000000000..a895ac74cab
--- /dev/null
+++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch
@@ -0,0 +1,15 @@
+don't install pre-compiled 'bedtools' binary, since BEDTools is provided as a proper dependency via EasyBuild
+author: Kenneth Hoste (HPC-UGent)
+--- ngs-smap-4.6.5/setup.cfg.orig	2022-10-11 09:59:22.522325500 +0200
++++ ngs-smap-4.6.5/setup.cfg	2023-04-07 16:48:58.434620448 +0200
+@@ -49,10 +49,6 @@
+ 	sphinx_rtd_theme~=1.0.0
+ 	sphinx-tabs~=3.2.0
+ 
+-[options.data_files]
+-bin = 
+-	bin/bedtools
+-
+ [egg_info]
+ tag_build = 
+ tag_date = 0

From 637f36b8748747e63d85c6eb66c7877f0c46c98f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Apr 2023 10:47:42 +0200
Subject: [PATCH 255/601] add Autotools build dependency for SMAP, required for
 isal

---
 easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb
index ecf81cc47c8..d72d6e89e6b 100644
--- a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb
@@ -8,6 +8,10 @@ description = "SMAP is an analysis tool for stack-based NGS read mapping"
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
+builddependencies = [
+    ('Autotools', '20220317'),  # required for isal
+]
+
 dependencies = [
     ('Python', '3.10.4'),
     ('SciPy-bundle', '2022.05'),  # for pandas

From f4580f79340e4d036cd0d9f43b6f54b936335d6e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sat, 8 Apr 2023 15:03:13 +0200
Subject: [PATCH 256/601] Patch UCC to support multiple component paths

---
 ...C-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb | 12 ++---
 .../u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb         |  6 ++-
 .../UCC-1.1.0-multiple_component_paths.patch  | 46 +++++++++++++++++++
 3 files changed, 55 insertions(+), 9 deletions(-)
 create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch

diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
index e607ff3eb14..f7b2a90b694 100644
--- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
+++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
@@ -42,20 +42,16 @@ dependencies = [
 
 preconfigopts = "./autogen.sh && "
 
-buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1'
-installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install'
-
-# UCC_COMPONENT_PATH completely overrides $EBROOTUCC/lib/ucc so install symbolic links
-# to existing non CUDA related components
-postinstallcmds = ['for i in $EBROOTUCC/lib/ucc/*; do ln -s $i %(installdir)s/lib/ucc; done']
+buildopts = '-C src/components/mc/cuda V=1 ' #&& make -C src/components/tl/nccl V=1'
+installopts = '-C src/components/mc/cuda ' #&& make -C src/components/tl/nccl install'
 
 sanity_check_paths = {
-    'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT],
+    'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT], #, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT],
     'dirs': ['lib']
 }
 
 sanity_check_commands = ["ucc_info -c"]
 
-modextravars = {'UCC_COMPONENT_PATH': '%(installdir)s/lib/ucc'}
+modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': '%(installdir)s/lib/ucc'}
 
 moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb
index b5ff6ef4e42..8c350bb641b 100644
--- a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb
@@ -14,7 +14,11 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/openucx/ucc/archive/refs/tags']
 sources = ['v%(version)s.tar.gz']
-checksums = ['74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7']
+patches = ['UCC-%(version)s-multiple_component_paths.patch']
+checksums = [
+    {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'},
+    {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'},
+]
 
 builddependencies = [
     ('binutils', '2.39'),
diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch
new file mode 100644
index 00000000000..0e13578b55f
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch
@@ -0,0 +1,46 @@
+Adds support for multiple extra components paths to UCC
+Was necessary to add, as they broke the logic we used for UCC_COMPONEN_PATH in 1.1.0,
+then removed it completely in 1.2.0.
+This patch also removes the need to copy over all the other plugins, thus supporting multiple external components.
+
+author: micketeer@gmail.com
+
+diff -ru ucc-1.1.0.orig/src/utils/ucc_component.c ucc-1.1.0.fixed/src/utils/ucc_component.c
+--- ucc-1.1.0.orig/src/utils/ucc_component.c	2023-04-06 15:16:18.341729973 +0200
++++ ucc-1.1.0.fixed/src/utils/ucc_component.c	2023-04-08 13:42:28.448319486 +0200
+@@ -128,6 +128,27 @@
+         return UCC_ERR_INVALID_PARAM;
+     }
+ 
++    char *extra_component_path = getenv("EB_UCC_EXTRA_COMPONENT_PATH");
++    if (extra_component_path) {
++        // Add extra room for extra paths, braces and comma (+3):
++        pattern_size =
++            strlen(ucc_global_config.component_path) + strlen(framework_name) + 16 + strlen(extra_component_path) + 3;
++        full_pattern = (char *)ucc_malloc(pattern_size, "full_pattern");
++        if (!full_pattern) {
++            ucc_error("failed to allocate %zd bytes for full_pattern",
++                      pattern_size);
++            return UCC_ERR_NO_MEMORY;
++        }
++        ucc_snprintf_safe(full_pattern, pattern_size, "{%s,%s}/libucc_%s_*.so",
++                          extra_component_path, ucc_global_config.component_path, framework_name);
++        // Replace ; typically used in PATHs variables with , for glob
++        char *current_pos = strchr(full_pattern, ';');
++        while (current_pos) {
++            *current_pos = ',';
++            current_pos = strchr(current_pos, ';');
++        }
++        glob(full_pattern, GLOB_BRACE, NULL, &globbuf);
++    } else {
+     pattern_size =
+         strlen(ucc_global_config.component_path) + strlen(framework_name) + 16;
+     full_pattern = (char *)ucc_malloc(pattern_size, "full_pattern");
+@@ -139,6 +160,7 @@
+     ucc_snprintf_safe(full_pattern, pattern_size, "%s/libucc_%s_*.so",
+                       ucc_global_config.component_path, framework_name);
+     glob(full_pattern, 0, NULL, &globbuf);
++    }
+     ucc_free(full_pattern);
+     n_loaded          = 0;
+ 

From b0138c820fde82995c901a131040efb80277ec0b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sat, 8 Apr 2023 16:06:32 +0200
Subject: [PATCH 257/601] Undo commented stuff in UCC-CUDA

---
 .../u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
index f7b2a90b694..971f57d306a 100644
--- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
+++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
@@ -42,11 +42,11 @@ dependencies = [
 
 preconfigopts = "./autogen.sh && "
 
-buildopts = '-C src/components/mc/cuda V=1 ' #&& make -C src/components/tl/nccl V=1'
-installopts = '-C src/components/mc/cuda ' #&& make -C src/components/tl/nccl install'
+buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1'
+installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install'
 
 sanity_check_paths = {
-    'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT], #, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT],
+    'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT],
     'dirs': ['lib']
 }
 

From 9a48138ce60f4c1469a03cd3df499328a3cce16e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sat, 8 Apr 2023 17:04:45 +0200
Subject: [PATCH 258/601] Fix relative path for new env var

---
 .../u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
index 971f57d306a..bfe211063d3 100644
--- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
+++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb
@@ -52,6 +52,6 @@ sanity_check_paths = {
 
 sanity_check_commands = ["ucc_info -c"]
 
-modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': '%(installdir)s/lib/ucc'}
+modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'}
 
 moduleclass = 'lib'

From dc7c31d6487cb8c9780acceade995f3162025a8b Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Sat, 8 Apr 2023 18:15:32 +0200
Subject: [PATCH 259/601] adding easyconfigs: astropy-4.2.1-foss-2020b.eb,
 astropy-4.2.1-intel-2020b.eb, astropy-5.2.2-gfbf-2022b.eb

---
 .../a/astropy/astropy-4.2.1-foss-2020b.eb     | 40 +++++++++++++++++++
 .../a/astropy/astropy-4.2.1-intel-2020b.eb    | 40 +++++++++++++++++++
 .../a/astropy/astropy-5.2.2-gfbf-2022b.eb     | 37 +++++++++++++++++
 3 files changed, 117 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb
 create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb
 create mode 100644 easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb

diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb
new file mode 100644
index 00000000000..879b5774c38
--- /dev/null
+++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'astropy'
+version = '4.2.1'
+
+homepage = 'https://www.astropy.org/'
+description = """The Astropy Project is a community effort to develop 
+a single core package for Astronomy in Python and foster interoperability 
+between Python astronomy packages."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+]
+
+use_pip = True
+
+sanity_pip_check = True
+
+exts_list = [
+    ('pyerfa', '1.7.3', {
+        'modulename': 'erfa',
+        'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'],
+    }),
+    ('extension-helpers', '0.1', {
+        'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'],
+    }),
+    (name, version, {
+        'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'],
+}
+
+moduleclass = 'astro'
diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb
new file mode 100644
index 00000000000..878eb8ce9fb
--- /dev/null
+++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'astropy'
+version = '4.2.1'
+
+homepage = 'https://www.astropy.org/'
+description = """The Astropy Project is a community effort to develop 
+a single core package for Astronomy in Python and foster interoperability 
+between Python astronomy packages."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+]
+
+use_pip = True
+
+sanity_pip_check = True
+
+exts_list = [
+    ('pyerfa', '1.7.3', {
+        'modulename': 'erfa',
+        'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'],
+    }),
+    ('extension-helpers', '0.1', {
+        'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'],
+    }),
+    (name, version, {
+        'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'],
+}
+
+moduleclass = 'astro'
diff --git a/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb b/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb
new file mode 100644
index 00000000000..16a33151336
--- /dev/null
+++ b/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb
@@ -0,0 +1,37 @@
+easyblock = "PythonBundle"
+
+name = 'astropy'
+version = '5.2.2'
+
+homepage = 'https://www.astropy.org/'
+description = """The Astropy Project is a community effort to develop a common 
+core package for Astronomy in Python and foster an ecosystem of interoperable 
+astronomy packages.
+
+The Astropy community is committed to supporting diversity and inclusion."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('PyYAML', '6.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pyerfa', '2.0.0.3', {
+        'modulename': 'erfa',
+        'checksums': ['d77fbbfa58350c194ccb99e5d93aa05d3c2b14d5aad8b662d93c6ad9fff41f39'],
+    }),
+    ('extension-helpers', '1.0.0', {
+        'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'],
+    }),
+    (name, version, {
+        'checksums': ['e6a9e34716bda5945788353c63f0644721ee7e5447d16b1cdcb58c48a96b0d9c'],
+    }),
+]
+
+moduleclass = 'astro'

From 96f28132496fed1a9a7d2fb7c50a355009e9441e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Apr 2023 18:27:23 +0200
Subject: [PATCH 260/601] {toolchain} intel/2023.03

---
 .../h/HPL/HPL-2.3-intel-2023.03.eb            | 21 ++++++++
 .../easyconfigs/i/iimpi/iimpi-2023.03.eb      | 18 +++++++
 .../imkl-FFTW-2023.1.0-iimpi-2023.03.eb       | 11 ++++
 easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb | 18 +++++++
 .../impi-2021.9.0-intel-compilers-2023.1.0.eb | 16 ++++++
 .../intel-compilers-2023.1.0.eb               | 37 +++++++++++++
 .../easyconfigs/i/intel/intel-2023.03.eb      | 22 ++++++++
 .../u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb        | 52 +++++++++++++++++++
 8 files changed, 195 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb
 create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb
 create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb
 create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb
 create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb
 create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb
 create mode 100644 easybuild/easyconfigs/i/intel/intel-2023.03.eb
 create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb
new file mode 100644
index 00000000000..10fe0118177
--- /dev/null
+++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb
@@ -0,0 +1,21 @@
+name = 'HPL'
+version = '2.3'
+
+homepage = 'https://www.netlib.org/benchmark/hpl/'
+description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits)
+ arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available
+ implementation of the High Performance Computing Linpack Benchmark."""
+
+toolchain = {'name': 'intel', 'version': '2023.03'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.netlib.org/benchmark/%(namelower)s']
+sources = [SOURCELOWER_TAR_GZ]
+# fix Make dependencies, so parallel build also works
+patches = ['HPL_parallel-make.patch']
+checksums = [
+    '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830',  # hpl-2.3.tar.gz
+    '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6',  # HPL_parallel-make.patch
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb
new file mode 100644
index 00000000000..0bb3e2c0aba
--- /dev/null
+++ b/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb
@@ -0,0 +1,18 @@
+# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild
+easyblock = 'Toolchain'
+
+name = 'iimpi'
+version = '2023.03'
+
+homepage = 'https://software.intel.com/parallel-studio-xe'
+description = """Intel C/C++ and Fortran compilers, alongside Intel MPI."""
+
+toolchain = SYSTEM
+
+local_comp_ver = '2023.1.0'
+dependencies = [
+    ('intel-compilers', local_comp_ver),
+    ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)),
+]
+
+moduleclass = 'toolchain'
diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb
new file mode 100644
index 00000000000..3809bf2daac
--- /dev/null
+++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb
@@ -0,0 +1,11 @@
+name = 'imkl-FFTW'
+version = '2023.1.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html'
+description = "FFTW interfaces using Intel oneAPI Math Kernel Library"
+
+toolchain = {'name': 'iimpi', 'version': '2023.03'}
+
+dependencies = [('imkl', version, '', SYSTEM)]
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb
new file mode 100644
index 00000000000..2dd371edc01
--- /dev/null
+++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb
@@ -0,0 +1,18 @@
+name = 'imkl'
+version = '2023.1.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html'
+description = "Intel oneAPI Math Kernel Library"
+
+toolchain = SYSTEM
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/']
+sources = ['l_onemkl_p_%(version)s.46342_offline.sh']
+checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167']
+
+interfaces = False
+
+installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log"
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb
new file mode 100644
index 00000000000..6e886d07ac1
--- /dev/null
+++ b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb
@@ -0,0 +1,16 @@
+name = 'impi'
+version = '2021.9.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html'
+description = "Intel MPI Library, compatible with MPICH ABI"
+
+toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'}
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/']
+sources = ['l_mpi_oneapi_p_%(version)s.43482_offline.sh']
+checksums = ['5c170cdf26901311408809ced28498b630a494428703685203ceef6e62735ef8']
+
+dependencies = [('UCX', '1.14.0')]
+
+moduleclass = 'mpi'
diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb
new file mode 100644
index 00000000000..91d2ec40b6e
--- /dev/null
+++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb
@@ -0,0 +1,37 @@
+name = 'intel-compilers'
+version = '2023.1.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html'
+description = "Intel C, C++ & Fortran compilers (classic and oneAPI)"
+
+toolchain = SYSTEM
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+sources = [
+    {
+        'source_urls': [
+            'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/89283df8-c667-47b0-b7e1-c4573e37bd3e/',
+        ],
+        'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.46347_offline.sh',
+    },
+    {
+        'source_urls': [
+            'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/150e0430-63df-48a0-8469-ecebff0a1858/',
+        ],
+        'filename': 'l_fortran-compiler_p_%(version)s.46348_offline.sh',
+    },
+]
+checksums = [
+    {'l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh':
+     '3ac1c1179501a2646cbb052b05426554194573b4f8e2344d7699eed03fbcfa1d'},
+    {'l_fortran-compiler_p_2023.1.0.46348_offline.sh':
+     '7639af4b6c928e9e3ba92297a054f78a55f4f4d0db9db0d144cc6653004e4f24'},
+]
+
+local_gccver = '12.2.0'
+dependencies = [
+    ('GCCcore', local_gccver),
+    ('binutils', '2.39', '', ('GCCcore', local_gccver)),
+]
+
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/i/intel/intel-2023.03.eb b/easybuild/easyconfigs/i/intel/intel-2023.03.eb
new file mode 100644
index 00000000000..9c71d4bc13e
--- /dev/null
+++ b/easybuild/easyconfigs/i/intel/intel-2023.03.eb
@@ -0,0 +1,22 @@
+easyblock = 'Toolchain'
+
+name = 'intel'
+version = '2023.03'
+
+homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain'
+description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)."
+
+toolchain = SYSTEM
+
+local_comp_ver = '2023.1.0'
+local_gccver = '12.2.0'
+dependencies = [
+    ('GCCcore', local_gccver),
+    ('binutils', '2.39', '', ('GCCcore', local_gccver)),
+    ('intel-compilers', local_comp_ver),
+    ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)),
+    ('imkl', local_comp_ver, '', SYSTEM),
+    ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)),
+]
+
+moduleclass = 'toolchain'
diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..c84b1e48791
--- /dev/null
+++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb
@@ -0,0 +1,52 @@
+easyblock = 'ConfigureMake'
+
+name = 'UCX'
+version = '1.14.0'
+
+homepage = 'https://www.openucx.org/'
+description = """Unified Communication X
+An open-source production grade communication framework for data centric
+and high-performance applications
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+patches = [
+    'UCX-1.13.1-dynamic_modules.patch',
+]
+checksums = [
+    {'ucx-1.14.0.tar.gz': '9bd95e2059de5dece9dddd049aacfca3d21bfca025748a6a0b1be4486e28afdd'},
+    {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'},
+]
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('Autotools', '20220317'),
+    ('pkgconf', '1.9.3'),
+]
+
+osdependencies = [OS_PKG_IBVERBS_DEV]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('numactl', '2.0.16'),
+]
+
+configure_cmd = "contrib/configure-release"
+
+configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs '
+configopts += '--without-java --without-go --disable-doxygen-doc '
+
+buildopts = 'V=1'
+
+sanity_check_paths = {
+    'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'],
+    'dirs': ['include', 'lib', 'share']
+}
+
+sanity_check_commands = ["ucx_info -d"]
+
+moduleclass = 'lib'

From e1ff56a686022bea3adbe2488f5659d6f2a985af Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Apr 2023 18:40:17 +0200
Subject: [PATCH 261/601] adding easyconfigs:
 sceasy-0.0.7-foss-2022a-R-4.2.1.eb, loompy-3.0.7-foss-2022a.eb,
 anndata-0.8.0-foss-2022a.eb

---
 .../a/anndata/anndata-0.8.0-foss-2022a.eb     | 38 ++++++++++++++++++
 .../l/loompy/loompy-3.0.7-foss-2022a.eb       | 39 +++++++++++++++++++
 .../sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb | 34 ++++++++++++++++
 3 files changed, 111 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb
new file mode 100644
index 00000000000..38ef7f588ea
--- /dev/null
+++ b/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonBundle'
+
+name = 'anndata'
+version = '0.8.0'
+
+homepage = 'https://github.com/scverse/anndata'
+description = """anndata is a Python package for handling annotated data matrices in memory and on disk,
+ positioned between pandas and xarray"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('h5py', '3.7.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('natsort', '8.3.1', {
+        'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'],
+    }),
+    (name, version, {
+        'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/natsort'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["natsort --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb
new file mode 100644
index 00000000000..a718a90a243
--- /dev/null
+++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb
@@ -0,0 +1,39 @@
+easyblock = 'PythonBundle'
+
+name = 'loompy'
+version = '3.0.7'
+
+homepage = 'https://loompy.org/'
+description = "Python implementation of the Loom file format, an efficient file format for large omics datasets"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('h5py', '3.7.0'),
+    ('numba', '0.56.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('numpy-groupies', '0.9.20', {
+        'sources': ['numpy_groupies-%(version)s.tar.gz'],
+        'checksums': ['923a382d6bc6876384b58a9c0503b05b9d36a660f329695c2d33e4f93fcbbe3d'],
+    }),
+    (name, version, {
+        'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/loompy'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["loompy --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..b20476c22cc
--- /dev/null
+++ b/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,34 @@
+easyblock = 'RPackage'
+
+name = 'sceasy'
+version = '0.0.7'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/cellgeni/sceasy'
+description = "sceasy is a package that helps easy conversion of different single-cell data formats to each other"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/cellgeni/sceasy/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['bc6a2dba2111067f3247ff1ee617cc85ab6c7d89950f7d8ca486a3e34b27f9d6']
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('R-bundle-Bioconductor', '3.15', versionsuffix),
+    ('Seurat', '4.3.0', versionsuffix),
+    ('anndata', '0.8.0'),
+    ('loompy', '3.0.7'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+sanity_check_commands = [
+    """echo "library(reticulate); reticulate::import('anndata');" | R -q --no-save""",
+    """echo "library(reticulate); reticulate::import('loompy');" | R -q --no-save""",
+]
+
+moduleclass = 'bio'

From 5a02c19e20059754d3f3e04593b3b85d336212a3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Apr 2023 19:06:00 +0200
Subject: [PATCH 262/601] adding easyconfigs: infercnvpy-0.4.2-foss-2022a.eb

---
 .../infercnvpy/infercnvpy-0.4.2-foss-2022a.eb | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb
new file mode 100644
index 00000000000..58e1804543b
--- /dev/null
+++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb
@@ -0,0 +1,51 @@
+easyblock = 'PythonBundle'
+
+name = 'infercnvpy'
+version = '0.4.2'
+
+homepage = 'https://github.com/icbi-lab/infercnvpy'
+description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('tqdm', '4.64.0'),
+    ('IPython', '8.5.0'),
+    ('leidenalg', '0.9.1'),
+    ('scanpy', '1.9.1'),
+    ('polars', '0.15.6'),  # required by gtfparse
+]
+
+use_pip = True
+
+# avoid hatchling requirement to install infercnvpy
+# (since installing it introduces conflicting version requirements with poetry included with Python)
+local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """
+local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """
+local_preinstallopts += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """
+
+exts_list = [
+    ('setuptools', '67.6.1', {
+        'checksums': ['257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a'],
+    }),
+    ('gtfparse', '2.0.1', {
+        'checksums': ['c45439af58cb48120910bebe4625371d8fb5735f12a749e8933c9d6f2b1a558c'],
+    }),
+    ('pyreadr', '0.4.7', {
+        'checksums': ['901110d62b4bedaef288f4db81425fb696edc721fe2c34c1083f5fb11050a73c'],
+    }),
+    ('session-info', '1.0.0', {
+        'sources': ['session_info-%(version)s.tar.gz'],
+        'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'],
+    }),
+    (name, version, {
+        'checksums': ['3cfd23afc2dbbca3508a305032c032440d2af292d037d43a7b5046c7bd36ed22'],
+        'preinstallopts': local_preinstallopts,
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From dc8e96c889bcb4dad2db713d1464b61767295bba Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 16:07:48 +0200
Subject: [PATCH 263/601] add local::lib extension to recent Perl easyconfigs

---
 easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++
 easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 5 +++++
 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 5 +++++
 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 5 +++++
 4 files changed, 20 insertions(+)

diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb
index 1211efd9bff..6f534c52ba2 100644
--- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb
@@ -1834,6 +1834,11 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'],
         'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'],
     }),
+    ('local::lib', '2.000029', {
+        'source_tmpl': 'local-lib-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'],
+        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
+    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb
index 1750e4abff0..be9cf2ec1fc 100644
--- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb
@@ -1944,6 +1944,11 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'],
         'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'],
     }),
+    ('local::lib', '2.000029', {
+        'source_tmpl': 'local-lib-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'],
+        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
+    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb
index 78044193927..00c76287298 100644
--- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb
+++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb
@@ -1934,6 +1934,11 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'],
         'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'],
     }),
+    ('local::lib', '2.000029', {
+        'source_tmpl': 'local-lib-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'],
+        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
+    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb
index 6a7989e6d2a..68757e61f49 100644
--- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb
@@ -1944,6 +1944,11 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'],
         'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'],
     }),
+    ('local::lib', '2.000029', {
+        'source_tmpl': 'local-lib-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'],
+        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
+    }),
 ]
 
 moduleclass = 'lang'

From 67820cf529c208e509da3c95b1b1a9debfbb3a55 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:03:24 +0200
Subject: [PATCH 264/601] adding easyconfigs: tRNAscan-SE-2.0.12-GCC-11.2.0.eb

---
 .../tRNAscan-SE-2.0.12-GCC-11.2.0.eb          | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb
new file mode 100644
index 00000000000..8260f1d0d1f
--- /dev/null
+++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'tRNAscan-SE'
+version = '2.0.12'
+
+homepage = 'https://github.com/UCSC-LoweLab/tRNAscan-SE'
+description = "A program for detection of tRNA genes"
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61']
+
+dependencies = [
+    ('Perl', '5.34.0'),
+]
+
+fix_perl_shebang_for = ['bin/*']
+
+sanity_check_paths = {
+    'files': ['bin/covels-SE', 'bin/tRNAscan-SE'],
+    'dirs': ['include', 'lib/tRNAscan-SE'],
+}
+
+sanity_check_commands = ["tRNAscan-SE --help"]
+
+moduleclass = 'bio'

From 4f06346ff13d745b873ad3afdf1ca2778033d558 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:03:38 +0200
Subject: [PATCH 265/601] adding easyconfigs: tantan-40-GCC-11.2.0.eb

---
 .../t/tantan/tantan-40-GCC-11.2.0.eb          | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb
new file mode 100644
index 00000000000..b6064225cd3
--- /dev/null
+++ b/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'tantan'
+version = '40'
+
+homepage = 'https://gitlab.com/mcfrith/tantan'
+description = "tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences"
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://gitlab.com/mcfrith/tantan/-/archive/%(version)s/']
+sources = ['tantan-%(version)s.tar.gz']
+checksums = ['61303c88cdf41fa5bcb5f77f674b4fac2a9bc0e4c9abb3b9d75af35c47162240']
+
+skipsteps = ['configure']
+
+installopts = "prefix=%(installdir)s"
+
+sanity_check_paths = {
+    'files': ['bin/tantan'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["tantan --help"]
+
+moduleclass = 'bio'

From 8a64df3179e5fe308d31f622595bc579d63bf46f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:03:52 +0200
Subject: [PATCH 266/601] adding easyconfigs: CodingQuarry-2.0-GCC-11.2.0.eb

---
 .../CodingQuarry-2.0-GCC-11.2.0.eb            | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb
new file mode 100644
index 00000000000..97fd89ed9c8
--- /dev/null
+++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'MakeCp'
+
+name = 'CodingQuarry'
+version = '2.0'
+
+homepage = 'https://sourceforge.net/p/codingquarry'
+description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts"
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['CodingQuarry_v%(version)s.tar.gz']
+checksums = ['1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504']
+
+buildopts = 'CFLAGS="$CFLAGS"'
+
+files_to_copy = [
+    (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'),
+    'QuarryFiles',
+]
+
+sanity_check_paths = {
+    'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'],
+    'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species'],
+}
+
+sanity_check_commands = ["CodingQuarry --help | grep '^CodingQuarry v. %(version)s'"]
+
+modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'}
+
+moduleclass = 'bio'

From 93abc67d12562ae911a14fbd75ea51de1eedc4e5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:04:06 +0200
Subject: [PATCH 267/601] adding easyconfigs: FASTA-36.3.8i-GCC-11.2.0.eb

---
 .../f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb       | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb
new file mode 100644
index 00000000000..ddc7db52078
--- /dev/null
+++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb
@@ -0,0 +1,36 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+
+easyblock = 'MakeCp'
+
+name = 'FASTA'
+version = '36.3.8i'
+local_version_date = '14-Nov-2020'
+
+homepage = 'http://fasta.bioch.virginia.edu'
+description = """The FASTA programs find regions of local or global (new) similarity between 
+protein or DNA sequences, either by searching Protein or DNA databases, or by identifying 
+local duplications within a sequence."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/wrpearson/fasta36/archive/']
+sources = ['v%%(version)s_%s.tar.gz' % local_version_date]
+checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008']
+
+buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all'
+
+files_to_copy = ['bin', 'conf', 'data', 'doc', 'FASTA_LIST', 'misc', 'README', 'seq', 'sql', 'test']
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"]
+
+sanity_check_paths = {
+    'files': ['FASTA_LIST', 'README'] + ['bin/fasta', 'bin/map_db'] +
+             ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf',
+                                                       'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch',
+                                                       'ssearch', 'tfastm', 'tfastx']],
+    'dirs': ['conf', 'data', 'doc', 'misc', 'seq', 'sql', 'test']
+}
+
+sanity_check_commands = ["fasta --help"]
+
+moduleclass = 'bio'

From abc0e1477b4e107588dd570b35d3369085f9dc7f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:04:19 +0200
Subject: [PATCH 268/601] adding easyconfigs: Proteinortho-6.2.3-gompi-2021b.eb

---
 .../Proteinortho-6.2.3-gompi-2021b.eb         | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb

diff --git a/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb
new file mode 100644
index 00000000000..524a8a0e657
--- /dev/null
+++ b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'Proteinortho'
+version = '6.2.3'
+
+homepage = 'https://www.bioinf.uni-leipzig.de/Software/proteinortho'
+description = "Proteinortho is a tool to detect orthologous genes within different species."
+
+toolchain = {'name': 'gompi', 'version': '2021b'}
+
+source_urls = ['https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/v%(version)s/']
+sources = ['proteinortho-v%(version)s.tar.gz']
+checksums = ['23079b3106deb41eab4a9123ea4744e9d05ab99e286184e617628fc243718dff']
+
+dependencies = [
+    ('Perl', '5.34.0'),
+    ('Python', '3.9.6'),
+    ('BLAST+', '2.12.0'),
+    ('DIAMOND', '2.0.13'),
+]
+
+skipsteps = ['configure']
+
+preinstallopts = "mkdir -p %(installdir)s/bin && "
+installopts = "PREFIX=%(installdir)s/bin"
+
+sanity_check_paths = {
+    'files': ['bin/proteinortho', 'bin/proteinortho%(version_major)s.pl', 'bin/proteinortho_clustering'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["proteinortho --help"]
+
+moduleclass = 'bio'

From 1b4a45c62d7deaf19125756c46dc8f011fef66e1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:06:50 +0200
Subject: [PATCH 269/601] adding easyconfigs: SignalP-6.0g-foss-2021b-fast.eb

---
 .../s/SignalP/SignalP-6.0g-foss-2021b-fast.eb | 51 +++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb

diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb
new file mode 100644
index 00000000000..6f37af3df3e
--- /dev/null
+++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb
@@ -0,0 +1,51 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+
+easyblock = 'PythonPackage'
+
+name = 'SignalP'
+version = '6.0g'
+_suffix = 'fast'
+versionsuffix = '-' + _suffix
+
+homepage = 'https://services.healthtech.dtu.dk/software.php'
+description = """SignalP predicts the presence  and  location of signal peptide  cleavage sites
+in  amino acid  sequences  from  different organisms"""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+download_instructions = """
+SignalP requires registration and acceptance of licence terms (academic use only).
+ [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0
+ [2] navigate to the "Downloads" tab
+ [3] select "%s" type under version "%%(version)s"
+ [4] complete the form; you should receive a download link via email
+""" % _suffix
+
+sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix]
+unpack_options = '--strip-components=1'
+checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa']
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),    # numpy > 1.19.2
+    ('tqdm', '4.62.3'),             # tqdm > 4.46.1
+    ('PyTorch', '1.12.1'),          # torch > 1.7.0
+    ('matplotlib', '3.5.2'),        # matplotlib > 3.3.2
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+_bin = '%%(namelower)s%s' % version[0]
+sanity_check_paths = {
+    'files': ['bin/%s' % _bin],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+sanity_check_commands = ['%s --help' % _bin]
+
+moduleclass = 'bio'

From 56812a347acbaaa87f229fe319425020fe399647 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:11:16 +0200
Subject: [PATCH 270/601] adding easyconfigs: SNAP-2.0.1-GCC-11.2.0.eb

---
 .../s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb           | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb
new file mode 100644
index 00000000000..ca3aa98f6b6
--- /dev/null
+++ b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'MakeCp'
+
+name = 'SNAP'
+version = '2.0.1'
+
+homepage = 'https://www.microsoft.com/en-us/research/project/snap'
+description = """Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for
+ high-throughput sequencing data"""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchainopts = {'cstd': 'c++98'}
+
+source_urls = ['https://github.com/amplab/snap/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['30f199c583e054c50ca6f3b61f27066640b7c829e5c5e8083841596a2869c064']
+
+dependencies = [('zlib', '1.2.11')]
+
+buildopts = 'CXX="$CXX"'
+
+files_to_copy = [(['snap-aligner', 'SNAPCommand'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/snap-aligner', 'bin/SNAPCommand'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["snap-aligner --help"]
+
+moduleclass = 'bio'

From 8cf43870add955e1599baa92092ca714a69b9383 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:11:30 +0200
Subject: [PATCH 271/601] adding easyconfigs: GlimmerHMM-3.0.4c-GCC-11.2.0.eb

---
 .../GlimmerHMM-3.0.4c-GCC-11.2.0.eb           | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb
new file mode 100644
index 00000000000..0935561b4ea
--- /dev/null
+++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb
@@ -0,0 +1,45 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+
+easyblock = 'MakeCp'
+
+name = 'GlimmerHMM'
+version = '3.0.4c'
+
+homepage = 'https://ccb.jhu.edu/software/glimmerhmm'
+description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model.
+ Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally
+ it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted
+ from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl']
+sources = [SOURCE_TAR_GZ]
+checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3']
+
+start_dir = 'sources'
+
+# make sure -O0 is not used as compiler option
+prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && "
+
+# also build in 'train' subdirectory to overwrite pre-compiled binaries
+buildopts = "&& cd ../train && make"
+
+local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp',
+                     'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP',
+                     'scoreSTOP2', 'splicescore', 'trainGlimmerHMM']
+files_to_copy = [
+    (['sources/%(namelower)s'], 'bin'),
+    (['train/%s' % x for x in local_train_files], 'bin'),
+    'trained_dir', 'README', 'train/readme.train',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['trained_dir'],
+}
+
+sanity_check_commands = ["%(namelower)s -h"]
+
+moduleclass = 'bio'

From 327f2e4403a3889b81456a5ff0e2e3f6ac278460 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:11:44 +0200
Subject: [PATCH 272/601] adding easyconfigs: trimAl-1.4.1-GCCcore-11.2.0.eb

---
 .../t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb   | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb
new file mode 100644
index 00000000000..3391b0d006e
--- /dev/null
+++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb
@@ -0,0 +1,37 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Updated by:
+# R.QIAO <rob.qiao@flinders.edu.au>
+# DeepThought, Flinders University
+
+easyblock = 'MakeCp'
+
+name = 'trimAl'
+version = '1.4.1'
+
+homepage = 'https://github.com/scapella/trimal'
+description = """EVB, FEP and LIE simulator."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'scapella'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e']
+
+builddependencies = [
+    ('binutils', '2.37'),
+
+]
+start_dir = 'source'
+
+files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/trimal', 'bin/readal', 'bin/statal'],
+    'dirs': []
+}
+
+sanity_check_commands = ["trimal -h"]
+
+moduleclass = 'bio'

From 15dd49714fdcc6dc827947794dc6deb28802dd25 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 18:35:37 +0200
Subject: [PATCH 273/601] remve duplicate local::lib from Perl easyconfigs

---
 easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 5 -----
 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 5 -----
 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 5 -----
 3 files changed, 15 deletions(-)

diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb
index be9cf2ec1fc..1750e4abff0 100644
--- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb
@@ -1944,11 +1944,6 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'],
         'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'],
     }),
-    ('local::lib', '2.000029', {
-        'source_tmpl': 'local-lib-%(version)s.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'],
-        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
-    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb
index 00c76287298..78044193927 100644
--- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb
+++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb
@@ -1934,11 +1934,6 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'],
         'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'],
     }),
-    ('local::lib', '2.000029', {
-        'source_tmpl': 'local-lib-%(version)s.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'],
-        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
-    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb
index 68757e61f49..6a7989e6d2a 100644
--- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb
@@ -1944,11 +1944,6 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'],
         'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'],
     }),
-    ('local::lib', '2.000029', {
-        'source_tmpl': 'local-lib-%(version)s.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'],
-        'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'],
-    }),
 ]
 
 moduleclass = 'lang'

From dc433c76e599ee5672e67318b7eb9cfd57129128 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 19:07:32 +0200
Subject: [PATCH 274/601] revert accidental changes to
 FASTX-Toolkit-0.0.14-GCC-11.3.0.eb

---
 .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb        | 34 +++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
index 67d8cb141e8..8589f7ecedc 100644
--- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb
@@ -8,8 +8,6 @@
 #
 # This work implements a part of the HPCBIOS project and is a component of the policy:
 # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
-#
-# Updated: Denis Kristak (Inuits)
 ##
 
 easyblock = 'Bundle'
@@ -26,6 +24,11 @@ toolchainopts = {'pic': True}
 
 default_easyblock = 'ConfigureMake'
 
+dependencies = [
+    ('GDGraph', '1.56'),
+    ('Perl', '5.34.1'),
+]
+
 components = [
     ('libgtextutils', '0.7', {
         'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'],
@@ -47,6 +50,23 @@ components = [
     }),
 ]
 
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('PerlIO::gzip', '0.20', {
+        'source_tmpl': 'PerlIO-gzip-0.20.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'],
+        'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'],
+    }),
+]
+
+fix_perl_shebang_for = ['bin/*.pl']
+
+modextrapaths = {
+    'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'
+}
+
 sanity_check_paths = {
     'files':
         ['bin/fastx_%s' % x for x in
@@ -62,4 +82,14 @@ sanity_check_paths = {
     'dirs': []
 }
 
+sanity_check_commands = [
+    'fasta_clipping_histogram.pl',
+    'fasta_formatter -h',
+    'fastq_masker -h | grep "FASTX Toolkit %(version)s"',
+    'fastq_quality_boxplot_graph.sh',
+    'fastx_barcode_splitter.pl --help | grep "Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008"',
+    'fastx_clipper -h | grep "FASTX Toolkit %(version)s"',
+    'fastx_nucleotide_distribution_graph.sh',
+]
+
 moduleclass = 'bio'

From b54a4779523e6346ca60e3184895bd9baccde7ee Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 19:17:09 +0200
Subject: [PATCH 275/601] fix import statement for Markup from Jinja2 in vispr
 + enhance sanity check + rename patch to include version

---
 .../easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb   | 12 +++++++++---
 ... => vispr-0.4.14_fix_pandas_version_change.patch} |  3 ++-
 2 files changed, 11 insertions(+), 4 deletions(-)
 rename easybuild/easyconfigs/v/vispr/{vispr_fix_pandas_version_change.patch => vispr-0.4.14_fix_pandas_version_change.patch} (81%)

diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
index 855cc5ee79b..79f801ad1f9 100644
--- a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
+++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
@@ -14,10 +14,11 @@ VISPR - A visualization framework for CRISPR data.
 toolchain = {'name': 'foss', 'version': '2022a'}
 
 sources = ['%(name)s-%(version)s.tar.gz']
-patches = ['vispr_fix_pandas_version_change.patch']
+patches = ['vispr-0.4.14_fix_pandas_version_change.patch']
 checksums = [
     {'vispr-0.4.14.tar.gz': 'dc2cf6ac9c8930b0f1f1b3a2b7f57bfae180b2ac3674060123fd2d7fe10ccd82'},
-    {'vispr_fix_pandas_version_change.patch': '406c78092f1b06114602d37eb216ce24e1206b52461d0fc4270971ab80f10529'},
+    {'vispr-0.4.14_fix_pandas_version_change.patch':
+     'a5b5bb73b4d3dc4166c71ffd468496c19add46edec55029fe9f40e880a90e9a6'},
 ]
 
 dependencies = [
@@ -30,11 +31,16 @@ dependencies = [
 
 download_dep_fail = True
 use_pip = True
-sanity_pip_check = True
+
+preinstallopts = "sed -i 's/from jinja2 import Markup/from markupsafe import Markup/g' vispr/server.py && "
 
 sanity_check_paths = {
     'files': ['bin/vispr'],
     'dirs': [],
 }
 
+sanity_check_commands = ["vispr --help"]
+
+sanity_pip_check = True
+
 moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch
similarity index 81%
rename from easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch
rename to easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch
index 05275dcd59c..c6afe977cc9 100644
--- a/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch
+++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch
@@ -1,4 +1,5 @@
-# with more recent versions of Pandas, the imported error was moved to `pandas.errors`
+with more recent versions of Pandas, the imported error was moved to `pandas.errors`
+author: Denis Kristak (INUITS)
 diff -ruN vispr-0.4.14_orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py
 --- vispr-0.4.14_orig/vispr/results/rna.py	2023-03-24 13:10:57.148839548 +0000
 +++ vispr-0.4.14/vispr/results/rna.py	2023-03-24 13:11:14.032660055 +0000

From 2349d5332645f598c284abf213f2682f5101f13f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 19:30:43 +0200
Subject: [PATCH 276/601] add separate patch to fix yaml.load statements in
 vispr 0.4.14

---
 .../v/vispr/vispr-0.4.14-foss-2022a.eb        | 11 +++---
 .../v/vispr/vispr-0.4.14_fix-imports.patch    | 26 ++++++++++++++
 .../v/vispr/vispr-0.4.14_fix-yaml-load.patch  | 35 +++++++++++++++++++
 ...spr-0.4.14_fix_pandas_version_change.patch | 14 --------
 4 files changed, 67 insertions(+), 19 deletions(-)
 create mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch
 create mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch
 delete mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch

diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
index 79f801ad1f9..e06d4354bf0 100644
--- a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
+++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb
@@ -14,11 +14,14 @@ VISPR - A visualization framework for CRISPR data.
 toolchain = {'name': 'foss', 'version': '2022a'}
 
 sources = ['%(name)s-%(version)s.tar.gz']
-patches = ['vispr-0.4.14_fix_pandas_version_change.patch']
+patches = [
+    'vispr-0.4.14_fix-imports.patch',
+    'vispr-0.4.14_fix-yaml-load.patch',
+]
 checksums = [
     {'vispr-0.4.14.tar.gz': 'dc2cf6ac9c8930b0f1f1b3a2b7f57bfae180b2ac3674060123fd2d7fe10ccd82'},
-    {'vispr-0.4.14_fix_pandas_version_change.patch':
-     'a5b5bb73b4d3dc4166c71ffd468496c19add46edec55029fe9f40e880a90e9a6'},
+    {'vispr-0.4.14_fix-imports.patch': '2744d5636ebd6849fb0fc99ff102a8a0256bec3e592c323c24132f1e694baf67'},
+    {'vispr-0.4.14_fix-yaml-load.patch': '6b994103c621fafc084fc6c11f966367ffddc36ac20c0f9fc44ef0bb4360f977'},
 ]
 
 dependencies = [
@@ -32,8 +35,6 @@ dependencies = [
 download_dep_fail = True
 use_pip = True
 
-preinstallopts = "sed -i 's/from jinja2 import Markup/from markupsafe import Markup/g' vispr/server.py && "
-
 sanity_check_paths = {
     'files': ['bin/vispr'],
     'dirs': [],
diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch
new file mode 100644
index 00000000000..162193ecf1c
--- /dev/null
+++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch
@@ -0,0 +1,26 @@
+fix import statement for pandas and Jinja2
+author: Denis Kristak (INUITS) + Kenneth Hoste (HPC-UGent)
+diff -ru vispr-0.4.14.orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py
+--- vispr-0.4.14.orig/vispr/results/rna.py	2016-08-11 09:16:23.000000000 +0200
++++ vispr-0.4.14/vispr/results/rna.py	2023-04-10 19:19:07.488661966 +0200
+@@ -11,7 +11,7 @@
+ 
+ from flask import render_template
+ import pandas as pd
+-from pandas.io.common import EmptyDataError
++from pandas.errors import EmptyDataError
+ import numpy as np
+ from sklearn.decomposition import PCA
+ from scipy.cluster.hierarchy import average, leaves_list, dendrogram
+diff -ru vispr-0.4.14.orig/vispr/server.py vispr-0.4.14/vispr/server.py
+--- vispr-0.4.14.orig/vispr/server.py	2015-11-08 00:47:23.000000000 +0100
++++ vispr-0.4.14/vispr/server.py	2023-04-10 19:25:06.417148288 +0200
+@@ -10,7 +10,7 @@
+ 
+ import numpy as np
+ from flask import Flask, render_template, request, session, abort
+-from jinja2 import Markup
++from markupsafe import Markup
+ import yaml
+ 
+ from vispr import __version__
diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch
new file mode 100644
index 00000000000..16d9b65d1a1
--- /dev/null
+++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch
@@ -0,0 +1,35 @@
+fix use of yaml.load, 'Loader' argument is required in PyYAML >= 6.0 
+author: Kenneth Hoste (HPC-UGent)
+diff -ru vispr-0.4.14.orig/vispr/cli.py vispr-0.4.14/vispr/cli.py
+--- vispr-0.4.14.orig/vispr/cli.py	2017-02-15 14:38:22.000000000 +0100
++++ vispr-0.4.14/vispr/cli.py	2023-04-10 19:26:01.251360284 +0200
+@@ -37,7 +37,7 @@
+     print("Loading data.")
+     for path in configs:
+         with open(path) as f:
+-            config = yaml.load(f)
++            config = yaml.load(f, Loader=yaml.Loader)
+         try:
+             app.screens.add(config, parentdir=os.path.dirname(path))
+         except KeyError as e:
+@@ -91,7 +91,7 @@
+         os.makedirs(directory)
+ 
+     with open(configpath) as f:
+-        screen = Screen(yaml.load(f), parentdir=os.path.dirname(configpath))
++        screen = Screen(yaml.load(f, Loader=yaml.Loader), parentdir=os.path.dirname(configpath))
+ 
+     def write(json, name):
+         with open(prefix + name + ".vega.json", "w") as out:
+diff -ru vispr-0.4.14.orig/vispr/server.py vispr-0.4.14/vispr/server.py
+--- vispr-0.4.14.orig/vispr/server.py	2015-11-08 00:47:23.000000000 +0100
++++ vispr-0.4.14/vispr/server.py	2023-04-10 19:25:06.417148288 +0200
+@@ -20,7 +20,7 @@
+ app.jinja_env.lstrip_blocks = True
+ 
+ with open(os.path.join(os.path.dirname(__file__), "captions.yaml")) as f:
+-    CAPTIONS = yaml.load(f)
++    CAPTIONS = yaml.load(f, Loader=yaml.Loader)
+ 
+ 
+ @app.route("/ping")
diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch
deleted file mode 100644
index c6afe977cc9..00000000000
--- a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-with more recent versions of Pandas, the imported error was moved to `pandas.errors`
-author: Denis Kristak (INUITS)
-diff -ruN vispr-0.4.14_orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py
---- vispr-0.4.14_orig/vispr/results/rna.py	2023-03-24 13:10:57.148839548 +0000
-+++ vispr-0.4.14/vispr/results/rna.py	2023-03-24 13:11:14.032660055 +0000
-@@ -11,7 +11,7 @@
- 
- from flask import render_template
- import pandas as pd
--from pandas.io.common import EmptyDataError
-+from pandas.errors import EmptyDataError
- import numpy as np
- from sklearn.decomposition import PCA
- from scipy.cluster.hierarchy import average, leaves_list, dendrogram

From 5e13c679fe7ef2989ab576466372e731701990ee Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 20:57:42 +0200
Subject: [PATCH 277/601] add missing Perl dependency for GlimmerHMM, also copy
 Perl modules required by trainGlimmerHMM, add sanity check command for
 trainGlimmerHMM

---
 .../g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb   | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb
index 0935561b4ea..2abdf04dc93 100644
--- a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb
@@ -18,6 +18,10 @@ source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl']
 sources = [SOURCE_TAR_GZ]
 checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3']
 
+dependencies = [
+    ('Perl', '5.34.0'),
+]
+
 start_dir = 'sources'
 
 # make sure -O0 is not used as compiler option
@@ -32,14 +36,22 @@ local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfa
 files_to_copy = [
     (['sources/%(namelower)s'], 'bin'),
     (['train/%s' % x for x in local_train_files], 'bin'),
+    (['train/*.pm'], 'lib/perl%(perlmajver)s'),
     'trained_dir', 'README', 'train/readme.train',
 ]
 
+fix_perl_shebang_for = ['bin/trainGlimmerHMM']
+
 sanity_check_paths = {
     'files': ['bin/%(namelower)s'],
     'dirs': ['trained_dir'],
 }
 
-sanity_check_commands = ["%(namelower)s -h"]
+sanity_check_commands = [
+    "%(namelower)s -h",
+    r"trainGlimmerHMM -h 2>&1 | grep '^[ ]*Train GlimmerHMM module'",
+]
+
+modextrapaths = {'PERL5LIB': 'lib/perl%(perlmajver)s'}
 
 moduleclass = 'bio'

From 7f911010361805e1f3826814e63056d1c661f791 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 21:21:14 +0200
Subject: [PATCH 278/601] add Python dependency for CodingQuarry 2.0 + add
 patch to make included Python script compatible with Python 3.x + add sanity
 check command to test it

---
 .../CodingQuarry-2.0-GCC-11.2.0.eb            | 21 +++++++++++++---
 .../CodingQuarry-2.0_python3.patch            | 24 +++++++++++++++++++
 2 files changed, 42 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch

diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb
index 97fd89ed9c8..88e26640f3d 100644
--- a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb
@@ -11,21 +11,36 @@ toolchainopts = {'openmp': True}
 
 source_urls = [SOURCEFORGE_SOURCE]
 sources = ['CodingQuarry_v%(version)s.tar.gz']
-checksums = ['1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504']
+patches = ['CodingQuarry-2.0_python3.patch']
+checksums = [
+    {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'},
+    {'CodingQuarry-2.0_python3.patch': '70b63cad753ed644338bd5e26124381c266164af6d6dbf42dbc806dc3d71fcc1'},
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+]
 
 buildopts = 'CFLAGS="$CFLAGS"'
 
 files_to_copy = [
     (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'),
     'QuarryFiles',
+    'TESTING',
 ]
 
+fix_python_shebang_for = ['bin/CufflinksGTF_to_CodingQuarryGFF3.py']
+
 sanity_check_paths = {
     'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'],
-    'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species'],
+    'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species', 'TESTING'],
 }
 
-sanity_check_commands = ["CodingQuarry --help | grep '^CodingQuarry v. %(version)s'"]
+sanity_check_commands = [
+    "CodingQuarry --help | grep '^CodingQuarry v. %(version)s'",
+    "mkdir -p %(builddir)s && cp -a %(installdir)s/TESTING %(builddir)s/TESTING",
+    "cd %(builddir)s/TESTING && CufflinksGTF_to_CodingQuarryGFF3.py Sp_transcripts.gtf > test.gff3",
+]
 
 modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'}
 
diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch
new file mode 100644
index 00000000000..921ec4e6a02
--- /dev/null
+++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch
@@ -0,0 +1,24 @@
+make CufflinksGTF_to_CodingQuarryGFF3.py script compatible with Python 3.x
+author: Kenneth Hoste (HPC-UGent)
+--- CufflinksGTF_to_CodingQuarryGFF3.py.orig	2016-03-09 01:35:28.000000000 +0100
++++ CufflinksGTF_to_CodingQuarryGFF3.py	2023-04-10 21:10:51.666438036 +0200
+@@ -5,7 +5,7 @@
+ try :
+     myFile = open(sys.argv[1], 'rU')
+ except :
+-    print 'run: \n\npython CufflinksGTF_to_CodingQuarryGFF3.py transcripts.gtf > out.gff3\n'
++    print('run: \n\npython CufflinksGTF_to_CodingQuarryGFF3.py transcripts.gtf > out.gff3\n')
+     exit()
+ 
+ number = 0
+@@ -18,8 +18,8 @@
+             number += 1
+         else :
+             number = 1
+-        print '%s\t%s\texon\t%s\t%s\t%s\t%s\t%s\tID=exon:%s.%i;Parent=%s;' %  \
+-            (fields[0], fields[1], fields[3], fields[4], fields[5], fields[6], fields[7], details[3], number, details[3]) 
++        print('%s\t%s\texon\t%s\t%s\t%s\t%s\t%s\tID=exon:%s.%i;Parent=%s;' %  \
++            (fields[0], fields[1], fields[3], fields[4], fields[5], fields[6], fields[7], details[3], number, details[3]))
+         IDprev = details[3]
+ 
+ myFile.close()

From 7a983ccad111c9cccc3c4c17ff936361ce7b480e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 10 Apr 2023 21:33:15 +0200
Subject: [PATCH 279/601] add Biopython dependency for CodingQuarry 2.0 + bump
 toolchain to foss/2021b + enhance patch to make fastaTranslate.py script
 compatible with Python 3.x

---
 ...-GCC-11.2.0.eb => CodingQuarry-2.0-foss-2021b.eb} | 10 +++++++---
 .../c/CodingQuarry/CodingQuarry-2.0_python3.patch    | 12 ++++++++++++
 2 files changed, 19 insertions(+), 3 deletions(-)
 rename easybuild/easyconfigs/c/CodingQuarry/{CodingQuarry-2.0-GCC-11.2.0.eb => CodingQuarry-2.0-foss-2021b.eb} (81%)

diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb
similarity index 81%
rename from easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb
rename to easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb
index 88e26640f3d..a82e6498b5f 100644
--- a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb
@@ -6,7 +6,7 @@ version = '2.0'
 homepage = 'https://sourceforge.net/p/codingquarry'
 description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts"
 
-toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchain = {'name': 'foss', 'version': '2021b'}
 toolchainopts = {'openmp': True}
 
 source_urls = [SOURCEFORGE_SOURCE]
@@ -14,11 +14,12 @@ sources = ['CodingQuarry_v%(version)s.tar.gz']
 patches = ['CodingQuarry-2.0_python3.patch']
 checksums = [
     {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'},
-    {'CodingQuarry-2.0_python3.patch': '70b63cad753ed644338bd5e26124381c266164af6d6dbf42dbc806dc3d71fcc1'},
+    {'CodingQuarry-2.0_python3.patch': '8e1b117431d8b104f2114875d8f751aa91c1c3c1b0ddd5a4f85251605c2ab9df'},
 ]
 
 dependencies = [
     ('Python', '3.9.6'),
+    ('Biopython', '1.79'),
 ]
 
 buildopts = 'CFLAGS="$CFLAGS"'
@@ -29,7 +30,10 @@ files_to_copy = [
     'TESTING',
 ]
 
-fix_python_shebang_for = ['bin/CufflinksGTF_to_CodingQuarryGFF3.py']
+fix_python_shebang_for = [
+    'bin/CufflinksGTF_to_CodingQuarryGFF3.py',
+    'QuarryFiles/scripts/*.py',
+]
 
 sanity_check_paths = {
     'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'],
diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch
index 921ec4e6a02..ddf50218a42 100644
--- a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch
+++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch
@@ -22,3 +22,15 @@ author: Kenneth Hoste (HPC-UGent)
          IDprev = details[3]
  
  myFile.close()
+--- QuarryFiles/scripts/fastaTranslate.py.orig	2016-03-09 01:35:28.000000000 +0100
++++ QuarryFiles/scripts/fastaTranslate.py	2023-04-10 21:30:47.355740964 +0200
+@@ -33,7 +33,7 @@
+ 		else :
+ 			protein+='*'
+ 		i+=3
+-        print '>%s' % (record.id)
+-        print protein
++        print('>%s' % (record.id))
++        print(protein)
+ 
+ myFASTA.close()

From bd6c624e648dab3a9693d047129dcf9fe128371c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 08:42:10 +0200
Subject: [PATCH 280/601] skip two flaky tests for PyTorch/1.12.1-foss-2021b

---
 .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb      | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
index b4e4f83ca06..7c58b58e5fd 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
@@ -122,6 +122,12 @@ excluded_tests = {
     '': [
         # This test seems to take too long on NVIDIA Ampere at least.
         'distributed/test_distributed_spawn',
+        # failing on broadwell
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'test_native_mha',
+        # flaky test which fails on some systems,
+        # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/elastic/multiprocessing/api_test',
     ]
 }
 

From 39ebe1c6a21d141327a4da894e2192a0da1e689e Mon Sep 17 00:00:00 2001
From: ll4strw <lenocil@strw.leidenuniv.nl>
Date: Tue, 11 Apr 2023 09:40:34 +0200
Subject: [PATCH 281/601] Added build dependency for hierarchical module naming
 scheme

---
 easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb
index 0f78f6e8ed9..86ae2b180e9 100644
--- a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb
+++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb
@@ -14,6 +14,7 @@ sources = ['v%(version)s.tar.gz']
 checksums = ['3fdf5b100206953f674c94d40599bdb3ea255244dcc42fab0d75855ee3645581']
 
 builddependencies = [
+    ('GCCcore', '11.2.0'),  # required for hierarchical module naming scheme
     ('binutils', '2.37', '', ('GCCcore', '11.2.0')),
     ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')),
     ('ZeroMQ', '4.3.4', '', ('GCCcore', '11.2.0')),

From b7c176b29210e5b0c9945b826320a916de41b05a Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 11 Apr 2023 10:17:25 +0200
Subject: [PATCH 282/601] Add CUDA versionsuffix to OpenMM

---
 .../a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb       | 2 +-
 ...0.0-foss-2022a.eb => OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb} | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)
 rename easybuild/easyconfigs/o/OpenMM/{OpenMM-8.0.0-foss-2022a.eb => OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb} (98%)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
index 6818ca92607..c3d268ba085 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
@@ -29,7 +29,7 @@ dependencies = [
     ('UCX-CUDA', '1.12.1', versionsuffix),
     ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM),
     ('NCCL', '2.12.12', versionsuffix),
-    ('OpenMM', '8.0.0'),
+    ('OpenMM', '8.0.0', versionsuffix),
 ]
 
 # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb
similarity index 98%
rename from easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
rename to easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb
index 4d937a03a22..3e75fe7bcb3 100644
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb
@@ -9,6 +9,7 @@ easyblock = 'CMakeMake'
 
 name = 'OpenMM'
 version = '8.0.0'
+versionsuffix= '-CUDA-%(cudaver)s'
 
 homepage = 'https://openmm.org'
 description = "OpenMM is a toolkit for molecular simulation."

From 8af41430f7254629f502ca114493bd263e72390c Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 11 Apr 2023 10:59:14 +0200
Subject: [PATCH 283/601] Fix style

---
 .../easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb
index 3e75fe7bcb3..4215d0a143f 100644
--- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb
@@ -9,7 +9,7 @@ easyblock = 'CMakeMake'
 
 name = 'OpenMM'
 version = '8.0.0'
-versionsuffix= '-CUDA-%(cudaver)s'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://openmm.org'
 description = "OpenMM is a toolkit for molecular simulation."

From 736af1fdd8f6825551905c9eba999066f31b940f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 16:17:12 +0200
Subject: [PATCH 284/601] stick to matplotlib 3.4.3 as dependency for SignalP
 6.0g with foss/2021b

---
 easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb
index 6f37af3df3e..b2f900f3c4a 100644
--- a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb
+++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb
@@ -33,7 +33,7 @@ dependencies = [
     ('SciPy-bundle', '2021.10'),    # numpy > 1.19.2
     ('tqdm', '4.62.3'),             # tqdm > 4.46.1
     ('PyTorch', '1.12.1'),          # torch > 1.7.0
-    ('matplotlib', '3.5.2'),        # matplotlib > 3.3.2
+    ('matplotlib', '3.4.3'),        # matplotlib > 3.3.2
 ]
 
 use_pip = True

From ed3a7f58c94366ca08537b3cdf52494dab967d71 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 17:42:14 +0200
Subject: [PATCH 285/601] {bio}[GCC/11.3.0] biobambam2 v2.0.87, libmaus2
 v2.0.499

---
 .../biobambam2-2.0.87-GCC-11.3.0.eb           | 27 +++++++++++++++++++
 .../l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb | 22 +++++++++++++++
 2 files changed, 49 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb
new file mode 100644
index 00000000000..26c750c21c9
--- /dev/null
+++ b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'biobambam2'
+version = '2.0.87'
+
+homepage = 'https://github.com/gt1/biobambam2'
+description = "Tools for processing BAM files"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/gt1/biobambam2/archive/']
+sources = ['%(version)s-release-20180301132713.tar.gz']
+checksums = ['a90500e547465d8d0455bda7936e0b660c0fd3f1b243083ec0739527f802dcf4']
+
+dependencies = [
+    ('libmaus2', '2.0.499'),
+]
+
+configopts = "--with-libmaus2=$EBROOTLIBMAUS2"
+
+sanity_check_paths = {
+    'files': ['bin/bamcollate2', 'bin/bammarkduplicates', 'bin/bammaskflags', 'bin/bamrecompress',
+              'bin/bamsormadup', 'bin/bamsort', 'bin/bamtofastq'],
+    'dirs': ['share/man'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb
new file mode 100644
index 00000000000..5aa65b14cf1
--- /dev/null
+++ b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'libmaus2'
+version = '2.0.499'
+
+homepage = 'https://github.com/gt1/libmaus2'
+description = "libmaus2 is a collection of data structures and algorithms."
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/gt1/libmaus2/archive/']
+sources = ['%(version)s-release-20180606122508.tar.gz']
+checksums = ['5e3643bb14a3342b76b68592252f248e5e97725caffe6a6a3274563a0433338a']
+
+sanity_check_paths = {
+    'files': ['lib/libmaus2.a', 'lib/libmaus2.%s' % SHLIB_EXT,
+              'lib/libmaus2_simd_align_128.a', 'lib/libmaus2_simd_align_128.%s' % SHLIB_EXT,
+              'lib/libmaus2_simd_align_256.a', 'lib/libmaus2_simd_align_256.%s' % SHLIB_EXT],
+    'dirs': ['include/libmaus2'],
+}
+
+moduleclass = 'lib'

From 109c7f83949cdd5040fd54fc4c01ceca2273862c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 17:48:07 +0200
Subject: [PATCH 286/601] add sanity check commands for biobambam2

---
 .../b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb          | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb
index 26c750c21c9..62dfa0f74a1 100644
--- a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb
@@ -18,10 +18,14 @@ dependencies = [
 
 configopts = "--with-libmaus2=$EBROOTLIBMAUS2"
 
+local_binaries = ['bamcollate2', 'bammarkduplicates', 'bammaskflags', 'bamrecompress',
+                  'bamsormadup', 'bamsort', 'bamtofastq']
+
 sanity_check_paths = {
-    'files': ['bin/bamcollate2', 'bin/bammarkduplicates', 'bin/bammaskflags', 'bin/bamrecompress',
-              'bin/bamsormadup', 'bin/bamsort', 'bin/bamtofastq'],
+    'files': ['bin/%s' % x for x in local_binaries],
     'dirs': ['share/man'],
 }
 
+sanity_check_commands = ["%s --help" % x for x in local_binaries]
+
 moduleclass = 'bio'

From a7a807fdff5fa4b4c8dcdd304f8101c225b84546 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 18:35:46 +0200
Subject: [PATCH 287/601] add PMA/unikn/ppcor extensions to R 4.2.x easyconfigs

---
 easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 9 +++++++++
 easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 9 +++++++++
 easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 9 +++++++++
 3 files changed, 27 insertions(+)

diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb
index 6175f90d834..7f0e053f59b 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb
@@ -3360,6 +3360,15 @@ exts_list = [
     ('geeM', '0.10.1', {
         'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'],
     }),
+    ('PMA', '1.2.1', {
+        'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'],
+    }),
+    ('unikn', '0.8.0', {
+        'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'],
+    }),
+    ('ppcor', '1.1', {
+        'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
+    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
index 7829620a4a2..2efbf9482f0 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
@@ -3469,6 +3469,15 @@ exts_list = [
     ('dlm', '1.1-6', {
         'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'],
     }),
+    ('PMA', '1.2.1', {
+        'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'],
+    }),
+    ('unikn', '0.8.0', {
+        'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'],
+    }),
+    ('ppcor', '1.1', {
+        'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
+    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
index ae739c4baf5..f89a16e5c6d 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
@@ -3540,6 +3540,15 @@ exts_list = [
     ('dlm', '1.1-6', {
         'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'],
     }),
+    ('PMA', '1.2.1', {
+        'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'],
+    }),
+    ('unikn', '0.8.0', {
+        'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'],
+    }),
+    ('ppcor', '1.1', {
+        'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
+    }),
 ]
 
 moduleclass = 'lang'

From b0ca99edf8d2fc9a168cb9b51614366fd13f9de0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 18:36:33 +0200
Subject: [PATCH 288/601] adding easyconfigs:
 DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb

---
 ...IALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb

diff --git a/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb
new file mode 100644
index 00000000000..b2a1f818c5d
--- /dev/null
+++ b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'RPackage'
+
+name = 'DIALOGUE'
+local_commit = '7109f6a'
+# see DESCRIPTION to determine version,
+# but add date stamp of commit since version is not always bumped
+version = '1.0-20230228'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/livnatje/DIALOGUE'
+description = """DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to
+ identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = ['https://github.com/livnatje/DIALOGUE/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['28a57c61c6854ca4c54114a3067437de6cee0eb1090c46ea45619457affdfb08']
+
+dependencies = [
+    ('R', '4.2.0'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+moduleclass = 'bio'

From c6c4bb149603e666625392e4ad9f64a940abc24e Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Tue, 11 Apr 2023 19:42:09 +0200
Subject: [PATCH 289/601] fix homepage in ELPA easyconfigs (due to switch to
 new domain)

---
 .../e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb           | 2 +-
 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb     | 2 +-
 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb
index 6d9cb0dca9b..fe138398a7a 100644
--- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb
@@ -10,7 +10,7 @@ name = 'ELPA'
 version = '2022.05.001'
 versionsuffix = '-CUDA-%(cudaver)s'
 
-homepage = 'https://elpa.rzg.mpg.de'
+homepage = 'https://elpa.mpcdf.mpg.de'
 description = """Eigenvalue SoLvers for Petaflop-Applications."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb
index 54a1ab0f515..09d5330ca5b 100644
--- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb
+++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb
@@ -9,7 +9,7 @@
 name = 'ELPA'
 version = '2022.05.001'
 
-homepage = 'https://elpa.rzg.mpg.de'
+homepage = 'https://elpa.mpcdf.mpg.de'
 description = """Eigenvalue SoLvers for Petaflop-Applications."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb
index 6af27dad529..2da3666b859 100644
--- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb
+++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb
@@ -9,7 +9,7 @@
 name = 'ELPA'
 version = '2022.05.001'
 
-homepage = 'https://elpa.rzg.mpg.de'
+homepage = 'https://elpa.mpcdf.mpg.de'
 description = """Eigenvalue SoLvers for Petaflop-Applications."""
 
 toolchain = {'name': 'intel', 'version': '2022a'}

From 2addb7b2d3111454b424a57af7992f4f4dc0adb3 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Tue, 11 Apr 2023 19:44:26 +0200
Subject: [PATCH 290/601] adding easyconfigs: ELPA-2022.05.001-foss-2022b.eb,
 ELPA-2022.05.001-intel-2022b.eb, ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb

---
 ...ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb | 48 +++++++++++++++++++
 .../e/ELPA/ELPA-2022.05.001-foss-2022b.eb     | 43 +++++++++++++++++
 .../e/ELPA/ELPA-2022.05.001-intel-2022b.eb    | 47 ++++++++++++++++++
 3 files changed, 138 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb
 create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb

diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb
new file mode 100644
index 00000000000..0bf44c8db66
--- /dev/null
+++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb
@@ -0,0 +1,48 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Authors::   Inge Gutheil <i.gutheil@fz-juelich.de>, Alan O'Cais <a.ocais@fz-juelich.de>
+# License::   MIT/GPL
+#
+##
+
+name = 'ELPA'
+version = '2022.05.001'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://elpa.mpcdf.mpg.de/'
+description = """Eigenvalue SoLvers for Petaflop-Applications."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/']
+sources = ['elpa-new_release_%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch']
+checksums = [
+    {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'},
+    {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch':
+     '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'},
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    # remove_xcompiler script requires 'python' command,
+    ('Python', '3.10.8'),
+    ('Perl', '5.36.0'),
+]
+
+dependencies = [
+    ('CUDA', '12.0.0', '', SYSTEM)
+]
+
+preconfigopts = './autogen.sh && '
+preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && '
+preconfigopts += 'autoreconf && '
+
+# When building in parallel, the file test_setup_mpi.mod is sometimes
+# used before it is built, leading to an error.  This must be a bug in
+# the makefile affecting parallel builds.
+maxparallel = 1
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb
new file mode 100644
index 00000000000..c9bf9efef08
--- /dev/null
+++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb
@@ -0,0 +1,43 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Authors::   Inge Gutheil <i.gutheil@fz-juelich.de>, Alan O'Cais <a.ocais@fz-juelich.de>
+# License::   MIT/GPL
+#
+##
+
+name = 'ELPA'
+version = '2022.05.001'
+
+homepage = 'https://elpa.mpcdf.mpg.de/'
+description = """Eigenvalue SoLvers for Petaflop-Applications."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/']
+sources = ['elpa-new_release_%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch']
+checksums = [
+    {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'},
+    {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch':
+     '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'},
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    # remove_xcompiler script requires 'python' command,
+    ('Python', '3.10.8'),
+    ('Perl', '5.36.0'),
+]
+
+preconfigopts = './autogen.sh && '
+preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && '
+preconfigopts += 'autoreconf && '
+
+# When building in parallel, the file test_setup_mpi.mod is sometimes
+# used before it is built, leading to an error.  This must be a bug in
+# the makefile affecting parallel builds.
+maxparallel = 1
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb
new file mode 100644
index 00000000000..473b2dce033
--- /dev/null
+++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb
@@ -0,0 +1,47 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Authors::   Inge Gutheil <i.gutheil@fz-juelich.de>, Alan O'Cais <a.ocais@fz-juelich.de>
+# License::   MIT/GPL
+#
+##
+
+name = 'ELPA'
+version = '2022.05.001'
+
+homepage = 'https://elpa.mpcdf.mpg.de/'
+description = """Eigenvalue SoLvers for Petaflop-Applications."""
+
+toolchain = {'name': 'intel', 'version': '2022b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/']
+sources = ['elpa-new_release_%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch']
+checksums = [
+    {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'},
+    {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch':
+     '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'},
+]
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    # remove_xcompiler script requires 'python' command,
+    ('Python', '3.10.8'),
+    ('Perl', '5.36.0'),
+]
+
+preconfigopts = './autogen.sh && '
+preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && '
+preconfigopts += 'autoreconf && '
+# If the build is running in a batch job, make sure Intel libmpi does
+# not try to use Slurm to run the MPI_THREAD test code that ELPA's
+# configure is running without "mpirun".
+preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && '
+
+# When building in parallel, the file test_setup_mpi.mod is sometimes
+# used before it is built, leading to an error.  This must be a bug in
+# the makefile affecting parallel builds.
+maxparallel = 1
+
+moduleclass = 'math'

From 7694d11ca53bcabe3338de86f1ac248eabe68d37 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 21:38:19 +0200
Subject: [PATCH 291/601] remove PGPLOT with GCCcore/10.3.0, since we have no
 need for it (as dependency)

---
 .../p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb   | 59 -------------------
 1 file changed, 59 deletions(-)
 delete mode 100644 easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb

diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
deleted file mode 100644
index e71115ce833..00000000000
--- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb
+++ /dev/null
@@ -1,59 +0,0 @@
-# Contribution from Imperial College London (UK)
-# Uploaded by J. Sassmannshausen
-
-easyblock = 'CmdCp'
-
-name = 'PGPLOT'
-version = '5.2.2'
-
-homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/'
-description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, 
-device-independent graphics package for making simple scientific graphs. It is intended 
-for making graphical images of publication quality with minimum effort on the part of 
-the user. For most applications, the program can be device-independent, and the output 
-can be directed to the appropriate device at run time."""
-
-toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
-
-source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/']
-sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')]
-patches = ['pgplot-compiler-pgplot522.patch']
-
-checksums = [
-    'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
-    'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec',   # pgplot-compiler-pgplot522.patch
-]
-
-builddependencies = [
-    ('binutils', '2.36.1'),
-]
-
-dependencies = [
-    ('libpng', '1.6.37'),
-    ('zlib', '1.2.11'),
-    ('X11', '20210518'),
-]
-
-cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')]
-
-files_to_copy = [
-    (['pgdemo*'], 'bin'),
-    (['libpgplot.*', 'libcpgplot.*'], 'lib'),
-    (['grfont.dat'], 'share'),
-    (['cpgplot.h'], 'include'),
-]
-
-postinstallcmds = [
-    # create symlinks
-    "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && "
-    " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so"
-]
-
-sanity_check_paths = {
-    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT],
-    'dirs': []
-}
-
-modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'}
-
-moduleclass = 'vis'

From c074f0bb3110c27d9969c3d0b19dde3eca868bd4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 21:42:51 +0200
Subject: [PATCH 292/601] rename patch for PGPLOT 5.2.2 + clean up
 postinstallcmds + enhance sanity check

---
 .../p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb   | 20 ++++++++++---------
 ...=> PGPLOT-5.2.2_gfortran-deps-fixes.patch} |  0
 2 files changed, 11 insertions(+), 9 deletions(-)
 rename easybuild/easyconfigs/p/PGPLOT/{pgplot-compiler-pgplot522.patch => PGPLOT-5.2.2_gfortran-deps-fixes.patch} (100%)

diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
index 3ffb0eb70e6..4033ffc1c52 100644
--- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb
@@ -17,11 +17,10 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
 
 source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/']
 sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')]
-patches = ['pgplot-compiler-pgplot522.patch']
-
+patches = ['PGPLOT-5.2.2_gfortran-deps-fixes.patch']
 checksums = [
-    'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4',   # pgplot522.tar.gz
-    'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec',   # pgplot-compiler-pgplot522.patch
+    {'pgplot522.tar.gz': 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4'},
+    {'PGPLOT-5.2.2_gfortran-deps-fixes.patch': 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec'},
 ]
 
 builddependencies = [
@@ -43,15 +42,18 @@ files_to_copy = [
     (['cpgplot.h'], 'include'),
 ]
 
+# create .so symlinks for shared libraries
 postinstallcmds = [
-    # create symlinks
-    "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && "
-    " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so"
+    "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT),
+    "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s" % (SHLIB_EXT, SHLIB_EXT),
+    "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT),
+    "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s" % (SHLIB_EXT, SHLIB_EXT),
 ]
 
 sanity_check_paths = {
-    'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT],
-    'dirs': []
+    'files': ['include/cpgplot.h', 'lib/libpgplot.a', 'lib/libcpgplot.a',
+              'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT],
+    'dirs': ['bin'],
 }
 
 modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'}
diff --git a/easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2_gfortran-deps-fixes.patch
similarity index 100%
rename from easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch
rename to easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2_gfortran-deps-fixes.patch

From 259b0c94df31f5ff6ef1dc5ed39d54c4594ff8a5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 22:25:28 +0200
Subject: [PATCH 293/601] add sanity check command for WCSLIB

---
 easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb
index 782f085864d..68d5f0a82df 100644
--- a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb
@@ -38,4 +38,6 @@ sanity_check_paths = {
     'dirs': ['include'],
 }
 
+sanity_check_commands = ["wcsgrid --help 2>&1 | grep '^Usage: wcsgrid'"]
+
 moduleclass = 'geo'

From 70e7c9b1291bfdb87be5cc4eb81d0371faafb119 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 11 Apr 2023 22:44:23 +0200
Subject: [PATCH 294/601] adding easyconfigs: DBG2OLC-20200724-GCC-11.3.0.eb

---
 .../d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb  | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb
new file mode 100644
index 00000000000..0c8e9e7176c
--- /dev/null
+++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CmdCp'
+
+name = 'DBG2OLC'
+version = '20200724'
+local_commit = '9514828'
+
+homepage = 'https://github.com/yechengxi/DBG2OLC'
+description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation 
+ Sequencing Technologies"""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/']
+sources = ['%s.tar.gz' % local_commit]
+checksums = ['52a05518a377a2bd784265a8dc05c49009f858d4c1c893b4dddbb12106bc0f99']
+
+cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")]
+
+files_to_copy = [(['DBG2OLC'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/DBG2OLC'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["DBG2OLC 2>&1 | grep 'For third-gen sequencing: DBG2OLC'"]
+
+moduleclass = 'bio'

From 8834ee40a30093f464e4c2b66c29e560f054255c Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 12 Apr 2023 01:10:04 +0200
Subject: [PATCH 295/601] adding easyconfigs:
 jax-0.3.25-foss-2022a-CUDA-11.7.0.eb, jax-0.3.25-foss-2022a.eb and patches:
 jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch,
 jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch

---
 .../jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb  | 124 ++++++++++++++++++
 .../j/jax/jax-0.3.25-foss-2022a.eb            | 114 ++++++++++++++++
 ...p-qdwh-test-rank-deficient-deficient.patch |  14 ++
 ..._skip-test-bcoo-dot-general-cusparse.patch |  14 ++
 4 files changed, 266 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch
 create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch

diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..8c8935d85b4
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,124 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Updated by: Alex Domingo (Vrije Universiteit Brussel)
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.3.25'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://pypi.python.org/pypi/jax'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('Bazel', '5.1.1'),
+    ('pytest-xdist', '2.5.0'),
+    # git 2.x required to fetch repository 'io_bazel_rules_docker'
+    ('git', '2.36.0', '-nodocs'),
+    ('matplotlib', '3.5.2'),  # required for tests/lobpcg_test.py
+]
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM),
+    ('NCCL', '2.12.12', versionsuffix),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('flatbuffers-python', '2.0'),
+]
+
+# downloading TensorFlow tarball to avoid that Bazel downloads it during the build
+# note: this *must* be the exact same commit as used in WORKSPACE
+local_tf_commit = 'f0fe8d4c04fab1f157854a1aa3c136377901cdef'
+local_tf_dir = 'tensorflow-%s' % local_tf_commit
+local_tf_builddir = '%(builddir)s/' + local_tf_dir
+
+# replace remote TensorFlow repository with the local one from EB
+local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && "
+local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir
+
+use_pip = True
+
+default_easyblock = 'PythonPackage'
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'source_urls': [PYPI_SOURCE],
+    'start_dir': '%(name)s-%(version)s',
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+}
+
+components = [
+    ('absl-py', '1.3.0', {
+        'options': {'modulename': 'absl'},
+        'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'],
+    }),
+    ('jaxlib', version, {
+        'sources': [
+            '%(name)s-v%(version)s.tar.gz',
+            {
+                'download_filename': '%s.tar.gz' % local_tf_commit,
+                'filename': 'tensorflow-%s.tar.gz' % local_tf_commit,
+            }
+        ],
+        'source_urls': [
+            'https://github.com/google/jax/archive/',
+            'https://github.com/tensorflow/tensorflow/archive/'
+        ],
+        'patches': [
+            ('jaxlib_local-tensorflow-repo.sed', '.'),
+            ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir),
+        ],
+        'checksums': [
+            # jaxlib-v0.3.25.tar.gz
+            '73ebc7868631cd9d520385557bbd7f08762d748a5a6a1bebef0f3b8d7ba748ef',
+            # tensorflow-f0fe8d4c04fab1f157854a1aa3c136377901cdef.tar.gz
+            '9ebba3031e8a81993682e4b9e43891ebb8480b6287e635df8e7efaa45ab5ede7',
+            # jaxlib_local-tensorflow-repo.sed
+            'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5',
+            # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch
+            '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db',
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        'prebuildopts': local_jax_prebuildopts,
+    }),
+]
+
+exts_list = [
+    ('opt_einsum', '3.3.0', {
+        'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'],
+    }),
+    ('etils', '0.8.0', {
+        'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'patches': [
+            'jax-0.3.23_relax-testPoly5-tolerance.patch',
+            'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch',
+            'jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch',
+            'jax-0.4.4_cusparse.patch',
+        ],
+        'checksums': [
+            {'jax-v0.3.25.tar.gz': '49e8ce88ddd7dd0de86116c9d75d98a577a9061377ec423493fbac5ea29f79f0'},
+            {'jax-0.3.23_relax-testPoly5-tolerance.patch':
+             'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'},
+            {'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch':
+             '70f16f2dba03ab162ce6e13ea61774524b485e9630209bbd4bec81fd16c8812f'},
+            {'jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch':
+             '335a8e206d14338176bf4136a131afe5d7b75999ac2c67f0ae79031322e25936'},
+            {'jax-0.4.4_cusparse.patch': '7414115533cce9f37c60850c09c69563a0ed6477c73f03c4132b9c2ae75ae60f'},
+        ],
+        'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " +
+                   "JAX_ENABLE_X64=true pytest -vv tests",
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb
new file mode 100644
index 00000000000..fb821e58e1d
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb
@@ -0,0 +1,114 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Updated by: Alex Domingo (Vrije Universiteit Brussel)
+easyblock = 'PythonBundle'
+
+name = 'jax'
+version = '0.3.25'
+
+homepage = 'https://pypi.python.org/pypi/jax'
+description = """Composable transformations of Python+NumPy programs:
+differentiate, vectorize, JIT to GPU/TPU, and more"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('Bazel', '5.1.1'),
+    ('pytest-xdist', '2.5.0'),
+    # git 2.x required to fetch repository 'io_bazel_rules_docker'
+    ('git', '2.36.0', '-nodocs'),
+    ('matplotlib', '3.5.2'),  # required for tests/lobpcg_test.py
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('flatbuffers-python', '2.0'),
+]
+
+# downloading TensorFlow tarball to avoid that Bazel downloads it during the build
+# note: this *must* be the exact same commit as used in WORKSPACE
+local_tf_commit = 'f0fe8d4c04fab1f157854a1aa3c136377901cdef'
+local_tf_dir = 'tensorflow-%s' % local_tf_commit
+local_tf_builddir = '%(builddir)s/' + local_tf_dir
+
+# replace remote TensorFlow repository with the local one from EB
+local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && "
+local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir
+
+use_pip = True
+
+default_easyblock = 'PythonPackage'
+default_component_specs = {
+    'sources': [SOURCE_TAR_GZ],
+    'source_urls': [PYPI_SOURCE],
+    'start_dir': '%(name)s-%(version)s',
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'download_dep_fail': True,
+}
+
+components = [
+    ('absl-py', '1.3.0', {
+        'options': {'modulename': 'absl'},
+        'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'],
+    }),
+    ('jaxlib', version, {
+        'sources': [
+            '%(name)s-v%(version)s.tar.gz',
+            {
+                'download_filename': '%s.tar.gz' % local_tf_commit,
+                'filename': 'tensorflow-%s.tar.gz' % local_tf_commit,
+            }
+        ],
+        'source_urls': [
+            'https://github.com/google/jax/archive/',
+            'https://github.com/tensorflow/tensorflow/archive/'
+        ],
+        'patches': [
+            ('jaxlib_local-tensorflow-repo.sed', '.'),
+            ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir),
+        ],
+        'checksums': [
+            # jaxlib-v0.3.25.tar.gz
+            '73ebc7868631cd9d520385557bbd7f08762d748a5a6a1bebef0f3b8d7ba748ef',
+            # tensorflow-f0fe8d4c04fab1f157854a1aa3c136377901cdef.tar.gz
+            '9ebba3031e8a81993682e4b9e43891ebb8480b6287e635df8e7efaa45ab5ede7',
+            # jaxlib_local-tensorflow-repo.sed
+            'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5',
+            # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch
+            '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db',
+        ],
+        'start_dir': 'jax-jaxlib-v%(version)s',
+        'prebuildopts': local_jax_prebuildopts,
+    }),
+]
+
+exts_list = [
+    ('opt_einsum', '3.3.0', {
+        'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'],
+    }),
+    ('etils', '0.8.0', {
+        'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(name)s-v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/google/jax/archive/'],
+        'patches': [
+            'jax-0.3.23_relax-testPoly5-tolerance.patch',
+            'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch',
+        ],
+        'checksums': [
+            {'jax-v0.3.25.tar.gz': '49e8ce88ddd7dd0de86116c9d75d98a577a9061377ec423493fbac5ea29f79f0'},
+            {'jax-0.3.23_relax-testPoly5-tolerance.patch':
+             'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'},
+            {'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch':
+             '70f16f2dba03ab162ce6e13ea61774524b485e9630209bbd4bec81fd16c8812f'},
+        ],
+        'runtest': "pytest -n %(parallel)s tests",
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch
new file mode 100644
index 00000000000..50eef092964
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch
@@ -0,0 +1,14 @@
+This test is known to fail on certain CPU arquitectures
+see https://github.com/google/jax/issues/14793
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- tests/qdwh_test.py.orig	2023-04-06 10:38:07.838718000 +0200
++++ tests/qdwh_test.py	2023-04-06 10:38:24.168026081 +0200
+@@ -168,7 +168,7 @@
+     [dict(m=m, n=n) for m, n in [(10, 10), (8, 8)]],
+     log_cond=np.linspace(1, 4, 4),
+   )
+-  def testQdwhWithOnRankDeficientInput(self, m, n, log_cond):
++  def disabled_testQdwhWithOnRankDeficientInput(self, m, n, log_cond):
+     """Tests qdwh with rank-deficient input."""
+     a = jnp.triu(jnp.ones((m, n))).astype(_QDWH_TEST_DTYPE)
+ 
diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch
new file mode 100644
index 00000000000..8a70ed941cf
--- /dev/null
+++ b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch
@@ -0,0 +1,14 @@
+Skip flaky tests with cuSPARSE as its API is quite variable,
+might solve itself in future versions of CUDA or jax
+see https://github.com/google/jax/issues/14663
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- tests/sparse_test.py.orig	2023-04-06 23:41:58.192895000 +0200
++++ tests/sparse_test.py	2023-04-06 23:59:56.319161821 +0200
+@@ -1173,6 +1173,7 @@
+     ],
+     dtype=jtu.dtypes.floating + jtu.dtypes.complex,
+   )
++  @unittest.skip("CUSPARSE_OPERATION_NON_TRANSPOSE is not supported with CUSPARSE_SPMM_COO_ALG2 on CUDA 11.7.0")
+   def test_bcoo_dot_general_cusparse(
+     self, lhs_shape, rhs_shape, dtype, lhs_contracting, rhs_contracting):
+     rng = jtu.rand_small(self.rng())

From b0cad395b794c9bcd352bffca9e31899ca31cebb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 12 Apr 2023 11:07:24 +0200
Subject: [PATCH 296/601] improve sanity_check_paths for casacore 3.4.0

---
 .../easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb      | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
index 8c95efa1c75..aab5e755fdf 100644
--- a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb
@@ -40,8 +40,9 @@ configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev -DDATA_DIR=%(insta
 configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON '
 
 sanity_check_paths = {
-    'files': [('lib/libcasa_casa.%s', 'lib/libcasa_mirlib.%s' % SHLIB_EXT, 'lib64/libcasa_ms.%s' % SHLIB_EXT)],
-    'dirs': ['include/casacore'],
+    'files': ['lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT,
+              'lib/libcasa_ms.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include/casacore'],
 }
 
 moduleclass = 'lib'

From 4ca05dc7cc6ab887447f82f7f8639cbfa7a41189 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Wed, 12 Apr 2023 19:01:01 +0200
Subject: [PATCH 297/601] adding easyconfigs: spglib-2.0.2-GCCcore-11.3.0.eb,
 ShengBTE-1.5.0-foss-2022a.eb, thirdorder-1.1.1-foss-2022a.eb

---
 .../s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb   | 43 +++++++++++++++++++
 .../s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb   | 31 +++++++++++++
 .../thirdorder/thirdorder-1.1.1-foss-2022a.eb | 40 +++++++++++++++++
 3 files changed, 114 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb
new file mode 100644
index 00000000000..494b3757f7b
--- /dev/null
+++ b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb
@@ -0,0 +1,43 @@
+# Author: Jasper Grimm (UoY)
+
+easyblock = 'MakeCp'
+
+name = 'ShengBTE'
+version = '1.5.0'
+
+homepage = 'https://bitbucket.org/sousaw/shengbte'
+description = "A solver for the Boltzmann transport equation for phonons."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'openmp': True}
+
+bitbucket_account = 'sousaw'
+source_urls = [BITBUCKET_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['fc1299921aa5f8046473d0c73114b826f803650b9a44e94338eaeb13e9c67381']
+
+dependencies = [
+    ('spglib', '2.0.2'),
+]
+
+start_dir = 'Src'
+
+# strip "include arch.make" -- not needed as we already set necessary env vars
+prebuildopts = "sed -i 's/^include arch.make//' Makefile && "
+# -fallow-argument-mismatch needed for GCC 10+
+buildopts = '-j 1 LIBS="$LIBBLAS -lsymspg" FFLAGS="$FFLAGS -fallow-argument-mismatch"'
+
+local_tests = ["Test-%s" % x for x in ['QE', 'RTA', 'VASP']]
+
+files_to_copy = [([name], 'bin'), (['LICENSE', 'README.md'], 'share')] + local_tests
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': ['share'] + local_tests,
+}
+
+sanity_check_commands = [
+    "cd %%(builddir)s/*%%(namelower)s*/%s && %%(mpi_cmd_prefix)s %%(name)s" % x for x in local_tests
+]
+
+moduleclass = 'phys'
diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..256f29f77b5
--- /dev/null
+++ b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'spglib'
+version = '2.0.2'
+
+homepage = 'https://spglib.github.io/spglib/'
+description = """Spglib is a C library for finding and handling crystal symmetries."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/spglib/spglib/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['10e44a35099a0a5d0fc6ee0cdb39d472c23cb98b1f5167c0e2b08f6069f3db1e']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+
+postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"]
+
+sanity_check_paths = {
+    'files': [
+        'include/spglib.h',
+        'lib/libsymspg.a',
+        'lib/libsymspg.%s' % SHLIB_EXT
+    ],
+    'dirs': [],
+}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb
new file mode 100644
index 00000000000..9ef61b93414
--- /dev/null
+++ b/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonPackage'
+name = 'thirdorder'
+version = '1.1.1'
+
+homepage = 'https://bitbucket.org/sousaw/thirdorder/'
+description = """A Python script to help create input files for computing anhamonic
+interatomic force constants, harnessing the symmetries of the system to minimize the
+number of required DFT calculations. A second mode of operation allows the user to
+build the third-order IFC matrix from the results of those runs."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('spglib', '2.0.2'),
+]
+
+source_urls = ['https://bitbucket.org/sousaw/thirdorder/get/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['f95e6371d78231d68028ec4e28d1d45ce60b1093e64f87e4b0cdb259375cd0d4']
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+# Thirdorder need to be built using Cython and it needs to have a version in setup.py
+preinstallopts = r'sed -i -e "s/^USE_CYTHON.*/USE_CYTHON=True/" '
+preinstallopts += r'-e "s/^\(setup(.*\))$/\1, version=\"%(version)s\")/" setup.py && '
+
+options = {'modulename': 'thirdorder_core'}
+
+postinstallcmds = ["mkdir %(installdir)s/bin && cp thirdorder_*.py %(installdir)s/bin/"]
+
+sanity_check_paths = {
+    'files': ['bin/thirdorder_%s.py' % x for x in ["castep", "espresso", "vasp"]],
+    'dirs': ['bin', 'lib'],
+}
+
+moduleclass = 'chem'

From 60d597de08ed03222259bf1be6d2dce002387c43 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 12 Apr 2023 19:16:27 +0200
Subject: [PATCH 298/601] adding easyconfigs:
 buildenv-default-foss-2022b-CUDA-12.0.0.eb, buildenv-default-foss-2022b.eb,
 buildenv-default-intel-2022b.eb

---
 ...buildenv-default-foss-2022b-CUDA-12.0.0.eb | 20 +++++++++++++++++++
 .../b/buildenv/buildenv-default-foss-2022b.eb | 13 ++++++++++++
 .../buildenv/buildenv-default-intel-2022b.eb  | 13 ++++++++++++
 3 files changed, 46 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb
 create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb

diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb
new file mode 100644
index 00000000000..c3821707135
--- /dev/null
+++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb
@@ -0,0 +1,20 @@
+easyblock = 'BuildEnv'
+
+name = 'buildenv'
+version = 'default'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'None'
+description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that
+ you can use to easily transition between toolchains when building your software. To query the variables being set
+ please use: module show <this module name>"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('CUDA', '12.0.0', '', SYSTEM),
+    ('UCX-CUDA', '1.13.1', versionsuffix),
+    ('UCC-CUDA', '1.1.0', versionsuffix),
+]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb
new file mode 100644
index 00000000000..1638fdb195d
--- /dev/null
+++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb
@@ -0,0 +1,13 @@
+easyblock = 'BuildEnv'
+
+name = 'buildenv'
+version = 'default'
+
+homepage = 'None'
+description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that
+ you can use to easily transition between toolchains when building your software. To query the variables being set
+ please use: module show <this module name>"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb
new file mode 100644
index 00000000000..47b7eb84b22
--- /dev/null
+++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb
@@ -0,0 +1,13 @@
+easyblock = 'BuildEnv'
+
+name = 'buildenv'
+version = 'default'
+
+homepage = 'None'
+description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that
+ you can use to easily transition between toolchains when building your software. To query the variables being set
+ please use: module show <this module name>"""
+
+toolchain = {'name': 'intel', 'version': '2022b'}
+
+moduleclass = 'devel'

From f3a08eca112a5aab06cecd51bbb82303b4933c44 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 12 Apr 2023 19:39:27 +0200
Subject: [PATCH 299/601] adding easyconfigs: libxc-6.1.0-GCC-12.2.0.eb,
 libxc-6.1.0-intel-compilers-2022.2.1.eb

---
 .../l/libxc/libxc-6.1.0-GCC-12.2.0.eb         | 45 +++++++++++++++++++
 .../libxc-6.1.0-intel-compilers-2022.2.1.eb   | 45 +++++++++++++++++++
 2 files changed, 90 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb

diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
new file mode 100644
index 00000000000..14cd0a84781
--- /dev/null
+++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'CMakeMake'
+
+name = 'libxc'
+version = '6.1.0'
+
+homepage = 'https://www.tddft.org/programs/libxc'
+description = """Libxc is a library of exchange-correlation functionals for density-functional theory.
+ The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Perl', '5.36.0'),
+]
+
+separate_build_dir = True
+
+local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF"
+
+# perform iterative build to get both static and shared libraries
+configopts = [
+    local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF',
+    local_common_configopts + ' -DBUILD_SHARED_LIBS=ON',
+]
+
+parallel = 1
+
+# make sure that built libraries (libxc*.so*) in build directory are picked when running tests
+# this is required when RPATH linking is used
+pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && "
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/xc-info'] +
+             ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]],
+    'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'],
+}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
new file mode 100644
index 00000000000..0675ab1e243
--- /dev/null
+++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
@@ -0,0 +1,45 @@
+easyblock = 'CMakeMake'
+
+name = 'libxc'
+version = '6.1.0'
+
+homepage = 'https://www.tddft.org/programs/libxc'
+description = """Libxc is a library of exchange-correlation functionals for density-functional theory.
+ The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals."""
+
+toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'}
+
+source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('Perl', '5.36.0'),
+]
+
+separate_build_dir = True
+
+local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF"
+
+# perform iterative build to get both static and shared libraries
+configopts = [
+    local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF',
+    local_common_configopts + ' -DBUILD_SHARED_LIBS=ON',
+]
+
+parallel = 1
+
+# make sure that built libraries (libxc*.so*) in build directory are picked when running tests
+# this is required when RPATH linking is used
+pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && "
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/xc-info'] +
+             ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]],
+    'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'],
+}
+
+moduleclass = 'chem'

From 72ec416a8469379c9cbbd667b82fba69b47c61c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 12 Apr 2023 20:14:52 +0200
Subject: [PATCH 300/601] Fix sanity check to use lib/cmake/ dir

---
 easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb         | 2 +-
 .../easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
index 14cd0a84781..8177e558c29 100644
--- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
@@ -39,7 +39,7 @@ runtest = 'test'
 sanity_check_paths = {
     'files': ['bin/xc-info'] +
              ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]],
-    'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'],
+    'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'],
 }
 
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
index 0675ab1e243..7b8ab41914b 100644
--- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
+++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
@@ -39,7 +39,7 @@ runtest = 'test'
 sanity_check_paths = {
     'files': ['bin/xc-info'] +
              ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]],
-    'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'],
+    'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'],
 }
 
 moduleclass = 'chem'

From e86deaef7f1ca24b1ae078668628e157c59dc0d7 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 12 Apr 2023 23:11:19 +0200
Subject: [PATCH 301/601] add comment explaining runtest command to jax v0.3.25
 with CUDA

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 .../easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb  | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb
index 8c8935d85b4..4ddfd6746ec 100644
--- a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb
@@ -114,6 +114,12 @@ exts_list = [
              '335a8e206d14338176bf4136a131afe5d7b75999ac2c67f0ae79031322e25936'},
             {'jax-0.4.4_cusparse.patch': '7414115533cce9f37c60850c09c69563a0ed6477c73f03c4132b9c2ae75ae60f'},
         ],
+        # deliberately not testing in parallel, as that results in (additional) failing tests;
+        # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing,
+        # see https://github.com/google/jax/issues/7323 and
+        # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst;
+        # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs;
+        # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores;
         'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " +
                    "JAX_ENABLE_X64=true pytest -vv tests",
     }),

From 4af5a6c9fc62aeb32331674d22ab694d8934eed9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 13 Apr 2023 02:22:05 +0200
Subject: [PATCH 302/601] Add sanity check command

---
 easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb       | 4 ++--
 .../l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb           | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
index 8177e558c29..4549d2c41b2 100644
--- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb
@@ -18,8 +18,6 @@ builddependencies = [
     ('Perl', '5.36.0'),
 ]
 
-separate_build_dir = True
-
 local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF"
 
 # perform iterative build to get both static and shared libraries
@@ -42,4 +40,6 @@ sanity_check_paths = {
     'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'],
 }
 
+sanity_check_commands = ['xc-info 1']
+
 moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
index 7b8ab41914b..8973869bc36 100644
--- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
+++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb
@@ -18,8 +18,6 @@ builddependencies = [
     ('Perl', '5.36.0'),
 ]
 
-separate_build_dir = True
-
 local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF"
 
 # perform iterative build to get both static and shared libraries
@@ -42,4 +40,6 @@ sanity_check_paths = {
     'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'],
 }
 
+sanity_check_commands = ['xc-info 1']
+
 moduleclass = 'chem'

From a1f307ad2f143c353d0dcb33699c7a4d6b07797f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 13 Apr 2023 10:42:25 +0200
Subject: [PATCH 303/601] update jax dependency of AlphaFold 2.3.1 to 0.3.25

---
 .../a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
index c3d268ba085..6dc2fe0aa60 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb
@@ -25,7 +25,7 @@ dependencies = [
     ('HH-suite', '3.3.0'),
     ('HMMER', '3.3.2'),
     ('Kalign', '3.3.5'),
-    ('jax', '0.3.14', versionsuffix),  # also provides absl-py
+    ('jax', '0.3.25', versionsuffix),  # also provides absl-py
     ('UCX-CUDA', '1.12.1', versionsuffix),
     ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM),
     ('NCCL', '2.12.12', versionsuffix),

From a4ac0ff20bbfb20957e1f1e8b8e05028ae243e39 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terjekv@users.noreply.github.com>
Date: Thu, 13 Apr 2023 11:21:21 +0200
Subject: [PATCH 304/601] Update
 easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb

Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com>
---
 .../libWallModelledLES-0.6.1-foss-2021b.eb                   | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
index 0efcf31e2cf..fdb85787dae 100644
--- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
@@ -35,7 +35,10 @@ install_cmd += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && "
 install_cmd += "pwd && ls && ./Allwmake -j %(parallel)s "
 install_cmd += " && cp -av tests %(installdir)s "
 
-sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLES.so"]}
+sanity_check_paths = {
+    "files": ["lib/libWallModelledLES.%s" % SHLIB_EXT],
+    "dirs": ["tests"],
+}
 sanity_check_commands = [
     "source $FOAM_BASH && cd %(installdir)s/tests/testCases/channel_flow && pimpleFoam"
 ]

From 5da2c31ad6cffa86d8bc444b251874236ae914cb Mon Sep 17 00:00:00 2001
From: Jasper <65227842+jfgrimm@users.noreply.github.com>
Date: Thu, 13 Apr 2023 10:29:15 +0100
Subject: [PATCH 305/601] Update
 easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb

---
 .../l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
index fdb85787dae..41c152957ce 100644
--- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb
@@ -15,7 +15,7 @@ toolchain = {"name": "foss", "version": "2021b"}
 toolchainopts = {"cstd": "c++11", "vectorize": False}
 
 source_urls = ["https://bitbucket.org/lesituu/libwallmodelledles/get/"]
-sources = ["af3c659d16d54238364e8812ae8fbe3e46f5e656.tar.gz"]
+sources = ["v%(version)s.tar.gz"]
 checksums = ["06b2c06ef76b5247c0a0c0260ea1e4a58bed8e930d0a0add9fe60e626c4bc0f8"]
 
 dependencies = [

From 7ce1cff20ecb550368806057a36f672248b75a12 Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Thu, 13 Apr 2023 14:38:44 +0200
Subject: [PATCH 306/601] Add ESPResSo and deps for 2021a

---
 .../Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb | 29 ++++++++++++++
 .../c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb | 38 +++++++++++++++++++
 .../ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb    | 38 +++++++++++++++++++
 .../p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb      | 25 ++++++++++++
 4 files changed, 130 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb
 create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb
 create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb

diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb
new file mode 100644
index 00000000000..9a5bff9bd31
--- /dev/null
+++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb
@@ -0,0 +1,29 @@
+easyblock = 'EB_Boost'
+
+name = 'Boost.MPI'
+version = '1.76.0'
+
+homepage = 'https://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'gompi', 'version': '2021a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/']
+sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['7bd7ddceec1a1dfdcbdb3e609b60d01739c38390a5f956385a12f3122049f0ca']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.11'),
+    ('XZ', '5.2.5'),
+    ('zstd', '1.4.9'),
+    ('ICU', '69.1'),
+]
+
+configopts = '--without-libraries=python'
+
+boost_mpi = True
+tagged_layout = True
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb
new file mode 100644
index 00000000000..faff04ca575
--- /dev/null
+++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonPackage'
+
+name = 'Cython'
+version = '0.29.34'
+
+homepage = 'https://cython.org/'
+description = """
+Cython is an optimising static compiler for both the Python programming
+language and the extended Cython programming language (based on Pyrex).
+"""
+docurls = [
+    'https://cython.org/#documentation',
+    'https://github.com/cython/cython',
+]
+
+toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['1909688f5d7b521a60c396d20bba9e47a1b2d2784bfb085401e1e1e7d29a29a8']
+
+builddependencies = [('binutils', '2.36.1')]
+
+dependencies = [('Python', '3.9.5')]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    'cython --version',
+]
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..4cdcffd3901
--- /dev/null
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'ESPResSo'
+version = '4.2.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://espressomd.org/wordpress'
+description = """A software package for performing and analyzing scientific Molecular Dynamics simulations."""
+
+source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['e6e17fafa9ba80b46f542dc86e07677a8d641cfd0102ebc4db2f7ee47d5fb6f1']
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+builddependencies = [('CMake', '3.20.1')]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('CUDA', '11.3.1', '', SYSTEM),
+    ('SciPy-bundle', '2021.05'),
+    ('Boost.MPI', '1.76.0'),
+    ('Cython', '0.29.34'),
+    ('HDF5', '1.10.7'),
+    ('Mesa', '21.1.1'),
+    ('GSL', '2.7'),
+    ('IPython', '7.25.0'),
+    ('Pint', '0.20.1'),
+]
+
+configopts = ' -DCMAKE_SKIP_RPATH=OFF '
+
+separate_build_dir = True
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb
new file mode 100644
index 00000000000..36db893fe73
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'Pint'
+version = '0.20.1'
+
+homepage = 'https://github.com/hgrecco/pint'
+description = """Pint is a Python package to define, operate and
+manipulate physical quantities: the product of a numerical value and a
+unit of measurement. It allows arithmetic operations between them and
+conversions from and to different units."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067']
+
+builddependencies = [('binutils', '2.36.1')]
+
+dependencies = [('Python', '3.9.5')]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'numlib'

From e4090a57702f4c1e6126c6174f80d0526ea5130d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 13 Apr 2023 15:18:03 +0200
Subject: [PATCH 307/601] Update
 easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb

---
 .../d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb
index b2a1f818c5d..9b146a684ba 100644
--- a/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb
+++ b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb
@@ -2,7 +2,7 @@ easyblock = 'RPackage'
 
 name = 'DIALOGUE'
 local_commit = '7109f6a'
-# see DESCRIPTION to determine version,
+# see DESCRIPTION file in source to determine version,
 # but add date stamp of commit since version is not always bumped
 version = '1.0-20230228'
 versionsuffix = '-R-%(rver)s'

From a8ca4a2ecbb3a958cc4a56e9418b45dd28e16a34 Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Thu, 13 Apr 2023 15:20:58 +0200
Subject: [PATCH 308/601] use recommended Java dependency 11

- also SYSTEM instead of True
---
 ...re-uftp-1.4.2-Java-1.8.eb => unicore-uftp-1.4.2-Java-11.eb} | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)
 rename easybuild/easyconfigs/u/unicore-uftp/{unicore-uftp-1.4.2-Java-1.8.eb => unicore-uftp-1.4.2-Java-11.eb} (84%)

diff --git a/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb
similarity index 84%
rename from easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb
rename to easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb
index cc641945cc6..920e80869a6 100644
--- a/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb
+++ b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb
@@ -13,8 +13,7 @@ source_urls = ['https://downloads.sourceforge.net/project/unicore/Clients/UFTP-C
 sources = ['uftp-client-%(version)s-all.zip']
 checksums = ['49670714416077274a0dfdc261e5552bcabbdd5cc4454181a794158491524c54']
 
-# specify dependency on Java/1.8 "wrapper", rather than a specific Java version
-dependencies = [('Java', '1.8', '', True)]
+dependencies = [('Java', '11', '', SYSTEM)]
 
 postinstallcmds = ["chmod +x %(installdir)s/bin/uftp"]
 

From 675e1e2f6f6233384f8099133152c79c8f95575c Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 13 Apr 2023 14:37:33 +0100
Subject: [PATCH 309/601] adding easyconfigs: PICI-LIGGGHTS-3.8.1-foss-2022a.eb

---
 .../PICI-LIGGGHTS-3.8.1-foss-2022a.eb         | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb
new file mode 100644
index 00000000000..4c7f30339f9
--- /dev/null
+++ b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb
@@ -0,0 +1,48 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = 'CMakeMake'
+
+name = 'PICI-LIGGGHTS'
+version = '3.8.1'
+
+homepage = 'https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS'
+description = """UoB Postron Imaging Centre's Improved LIGGGHTS distribution with
+ an emphasis on the Python interface."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['49df8c0379b00ebb57eac7c8ec25755976c2459c0a9f569090b55a0aafee628f']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('libjpeg-turbo', '2.1.3'),
+    ('VTK', '9.2.2'),
+]
+
+configopts = '-DVTK_DIR=$EBROOTVTK'
+
+_pydir = "%(installdir)s/lib/python%(pyshortver)s/site-packages"
+postinstallcmds = [
+    "mkdir -p %s" % _pydir,
+    "cd %%(builddir)s/%%(name)s*/python && python install.py %%(installdir)s/lib %s" % _pydir,
+    "cp -r %(builddir)s/%(name)s*/examples %(installdir)s/",
+]
+start_dir = 'src'
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+sanity_check_paths = {
+    'files': ['bin/liggghts', 'lib/libliggghts.a', 'lib/libliggghts.%s' % SHLIB_EXT],
+    'dirs': ['examples/LIGGGHTS/Tutorials_public', 'include'],
+}
+
+sanity_check_commands = ['python -c "import liggghts"']
+
+moduleclass = 'cae'

From 399a01583ddfd34e189f46de83b83733c74ba4eb Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Thu, 13 Apr 2023 15:38:10 +0200
Subject: [PATCH 310/601] Add sanity check

---
 .../ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb       | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
index 4cdcffd3901..3dac9d9fef5 100644
--- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
@@ -35,4 +35,20 @@ separate_build_dir = True
 
 modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
 
+_binaries = ['ipypresso',  'pypresso']
+_libs = [
+    'Espresso_config.so', 'Espresso_core.so', 'Espresso_script_interface.so', 'Espresso_shapes.so',
+    '_init.so', 'analyze.so', 'code_info.so', 'cuda_init.so', 'electrokinetics.so', 'galilei.so',
+    'integrate.so', 'interactions.so', 'lb.so', 'particle_data.so', 'polymer.so', 'profiler.so',
+    'script_interface.so', 'system.so', 'thermostat.so', 'utils.so', 'version.so',
+]
+
+_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _binaries] +
+             [_lib_path + '/%s' % x for x in _libs],
+    'dirs': ['bin', 'lib']
+}
+
 moduleclass = 'chem'

From 8ee2b1cfbdec034a73190879ef4d1eaeec3d3dda Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Thu, 13 Apr 2023 17:21:27 +0200
Subject: [PATCH 311/601] Change filename

---
 ...-CUDA-11.7.0.eb => ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb} | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)
 rename easybuild/easyconfigs/e/ESPResSo/{ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb => ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb} (93%)

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
similarity index 93%
rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
rename to easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
index 3dac9d9fef5..f89a0dddce5 100644
--- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
@@ -29,7 +29,9 @@ dependencies = [
     ('Pint', '0.20.1'),
 ]
 
-configopts = ' -DCMAKE_SKIP_RPATH=OFF '
+configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON'
+
+buildopts = ' && make check_unit_tests && make check_python '
 
 separate_build_dir = True
 

From 674c3e0fa341f483bcc389270ab813f75dec39cb Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Thu, 13 Apr 2023 15:47:14 +0000
Subject: [PATCH 312/601] adding easyconfigs: ruffus-2.8.4-GCCcore-11.3.0.eb

---
 .../r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb   | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..d0606a41e97
--- /dev/null
+++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'ruffus'
+version = '2.8.4'
+
+homepage = 'http://www.ruffus.org.uk/'
+description = """Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly,
+ and widely used in science and bioinformatics."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Graphviz', '5.0.0'),
+]
+
+download_dep_fail = True
+
+use_pip = True
+sanity_pip_check = True
+
+
+sanity_check_commands = ["python -c 'import ruffus.graph'"]
+
+moduleclass = 'lib'

From f113a552daba71c4196a8e62ba3030b4008cd916 Mon Sep 17 00:00:00 2001
From: Maxim <maxim.vadimovich@gmail.com>
Date: Thu, 13 Apr 2023 18:28:48 +0200
Subject: [PATCH 313/601] Update ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb

---
 .../e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb           | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
index f89a0dddce5..51fa7dc8424 100644
--- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
@@ -31,8 +31,6 @@ dependencies = [
 
 configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON'
 
-buildopts = ' && make check_unit_tests && make check_python '
-
 separate_build_dir = True
 
 modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}

From bdca62103b6e42bfff2449a7a64e636e0a0b5e4a Mon Sep 17 00:00:00 2001
From: Maxim <maxim.vadimovich@gmail.com>
Date: Thu, 13 Apr 2023 18:29:58 +0200
Subject: [PATCH 314/601] Rename ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb to
 ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb

---
 ...1a-CUDA-11.3.1.eb => ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easybuild/easyconfigs/e/ESPResSo/{ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb => ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} (100%)

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb
similarity index 100%
rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
rename to easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb

From c802939db634b4e661dac25665b4b13f40ce5ab1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 13 Apr 2023 18:35:34 +0200
Subject: [PATCH 315/601] add patch for scipy 1.10.1 extension in SciPy-bundle
 2023.02 to fix broken test (fixes #17693)

---
 .../SciPy-bundle-2023.02-gfbf-2022b.eb        |   2 +
 .../scipy-1.10.1_fix-lobpcg-test.patch        | 185 ++++++++++++++++++
 2 files changed, 187 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
index f6d9d0f8045..171798e25d4 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
@@ -51,12 +51,14 @@ exts_list = [
         'patches': [
             'scipy-1.10.1_disable-tests.patch',
             'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch',
+            'scipy-1.10.1_fix-lobpcg-test.patch',
         ],
         'checksums': [
             {'scipy-1.10.1.tar.gz': '2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'},
             {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'},
             {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch':
              '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'},
+            {'scipy-1.10.1_fix-lobpcg-test.patch': '45d6c9e0241b9e5d035474033d0caacec705c58ad89e22419c62bef2b17ae8aa'},
         ],
         'enable_slow_tests': True,
         'ignore_test_result': False,
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
new file mode 100644
index 00000000000..f05389c915c
--- /dev/null
+++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
@@ -0,0 +1,185 @@
+see https://github.com/scipy/scipy/issues/17954 + https://github.com/scipy/scipy/pull/17975
+From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
+Date: Tue, 14 Feb 2023 17:09:13 -0500
+Subject: [PATCH 1/6] Update test_lobpcg.py
+
+test
+---
+ scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+index afd7a106ea0..8e6de348a34 100644
+--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+@@ -255,17 +255,16 @@ def test_fiedler_large_12():
+     _check_fiedler(12, 2)
+ 
+ 
+-@pytest.mark.skipif(platform.machine() == 'aarch64',
+-                    reason="issue #15935")
++@pytest.mark.filterwarnings("ignore:Failed at iteration")
+ def test_failure_to_run_iterations():
+     """Check that the code exists gracefully without breaking. Issue #10974.
++    The code may or not issue a warning, filtered out. Issue #15935, #17954.
+     """
+     rnd = np.random.RandomState(0)
+     X = rnd.standard_normal((100, 10))
+     A = X @ X.T
+     Q = rnd.standard_normal((X.shape[0], 4))
+-    with pytest.warns(UserWarning, match="Failed at iteration"):
+-        eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
++    eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
+     assert np.max(eigenvalues) > 0
+ 
+ 
+
+From ad2054168d1eb522cc9b71eebc9ea32aa0fbd4e3 Mon Sep 17 00:00:00 2001
+From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
+Date: Tue, 14 Feb 2023 18:14:37 -0500
+Subject: [PATCH 2/6] Update test_lobpcg.py
+
+"Exited at iteration" also needs filtering out
+---
+ scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+index 8e6de348a34..aa3a0c29842 100644
+--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+@@ -256,6 +256,7 @@ def test_fiedler_large_12():
+ 
+ 
+ @pytest.mark.filterwarnings("ignore:Failed at iteration")
++@pytest.mark.filterwarnings("ignore:Exited at iteration")
+ def test_failure_to_run_iterations():
+     """Check that the code exists gracefully without breaking. Issue #10974.
+     The code may or not issue a warning, filtered out. Issue #15935, #17954.
+
+From 5357bcbd970cdc6ef88be5e58ff3a46d34fde61e Mon Sep 17 00:00:00 2001
+From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
+Date: Tue, 14 Feb 2023 18:34:51 -0500
+Subject: [PATCH 3/6] Update test_lobpcg.py
+
+added one more filter
+@pytest.mark.filterwarnings("ignore:Exited postprocessing")
+---
+ scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+index aa3a0c29842..87f3756c37d 100644
+--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+@@ -257,6 +257,7 @@ def test_fiedler_large_12():
+ 
+ @pytest.mark.filterwarnings("ignore:Failed at iteration")
+ @pytest.mark.filterwarnings("ignore:Exited at iteration")
++@pytest.mark.filterwarnings("ignore:Exited postprocessing")
+ def test_failure_to_run_iterations():
+     """Check that the code exists gracefully without breaking. Issue #10974.
+     The code may or not issue a warning, filtered out. Issue #15935, #17954.
+
+From bcad369ce894320f310c761e0136816c0a1410fb Mon Sep 17 00:00:00 2001
+From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
+Date: Wed, 15 Feb 2023 07:59:37 -0500
+Subject: [PATCH 4/6] Update test_lobpcg.py
+
+as proposed by reviewer
+---
+ scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+index 87f3756c37d..936cc6f8db7 100644
+--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+@@ -255,9 +255,6 @@ def test_fiedler_large_12():
+     _check_fiedler(12, 2)
+ 
+ 
+-@pytest.mark.filterwarnings("ignore:Failed at iteration")
+-@pytest.mark.filterwarnings("ignore:Exited at iteration")
+-@pytest.mark.filterwarnings("ignore:Exited postprocessing")
+ def test_failure_to_run_iterations():
+     """Check that the code exists gracefully without breaking. Issue #10974.
+     The code may or not issue a warning, filtered out. Issue #15935, #17954.
+@@ -266,7 +263,9 @@ def test_failure_to_run_iterations():
+     X = rnd.standard_normal((100, 10))
+     A = X @ X.T
+     Q = rnd.standard_normal((X.shape[0], 4))
+-    eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
++    with warnings.catch_warnings():
++        warnings.simplefilter("ignore")
++        eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
+     assert np.max(eigenvalues) > 0
+ 
+ 
+
+From bf8f497984c2056819068d8da5231c1e430659b3 Mon Sep 17 00:00:00 2001
+From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
+Date: Wed, 15 Feb 2023 10:25:29 -0500
+Subject: [PATCH 5/6] Update test_lobpcg.py
+
+import warnings added
+---
+ scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+index 936cc6f8db7..db87940e6a8 100644
+--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+@@ -4,6 +4,7 @@
+ import itertools
+ import platform
+ import sys
++import warnings
+ import pytest
+ import numpy as np
+ from numpy import ones, r_, diag
+
+From 77b9f45041bcfcb8e531b4d44c0399f103850e4d Mon Sep 17 00:00:00 2001
+From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
+Date: Wed, 15 Feb 2023 11:51:01 -0500
+Subject: [PATCH 6/6] Update test_lobpcg.py
+
+fall back to what has passed
+---
+ scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 8 ++++----
+ 1 file changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+index db87940e6a8..87f3756c37d 100644
+--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
+@@ -4,7 +4,6 @@
+ import itertools
+ import platform
+ import sys
+-import warnings
+ import pytest
+ import numpy as np
+ from numpy import ones, r_, diag
+@@ -256,6 +255,9 @@ def test_fiedler_large_12():
+     _check_fiedler(12, 2)
+ 
+ 
++@pytest.mark.filterwarnings("ignore:Failed at iteration")
++@pytest.mark.filterwarnings("ignore:Exited at iteration")
++@pytest.mark.filterwarnings("ignore:Exited postprocessing")
+ def test_failure_to_run_iterations():
+     """Check that the code exists gracefully without breaking. Issue #10974.
+     The code may or not issue a warning, filtered out. Issue #15935, #17954.
+@@ -264,9 +266,7 @@ def test_failure_to_run_iterations():
+     X = rnd.standard_normal((100, 10))
+     A = X @ X.T
+     Q = rnd.standard_normal((X.shape[0], 4))
+-    with warnings.catch_warnings():
+-        warnings.simplefilter("ignore")
+-        eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
++    eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
+     assert np.max(eigenvalues) > 0
+ 
+ 

From 157c9349492d346f662ca453d6e648124c758619 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 13 Apr 2023 18:25:45 +0100
Subject: [PATCH 316/601] generate patch that applies

---
 .../SciPy-bundle-2023.02-gfbf-2022b.eb        |   2 +-
 .../scipy-1.10.1_fix-lobpcg-test.patch        | 170 +-----------------
 2 files changed, 8 insertions(+), 164 deletions(-)

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
index 171798e25d4..ec4572d24d0 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
@@ -58,7 +58,7 @@ exts_list = [
             {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'},
             {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch':
              '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'},
-            {'scipy-1.10.1_fix-lobpcg-test.patch': '45d6c9e0241b9e5d035474033d0caacec705c58ad89e22419c62bef2b17ae8aa'},
+            {'scipy-1.10.1_fix-lobpcg-test.patch': '4940d3856d66f88af4b242dcd3b83f83a9b30da36ead73776f8d72cc17c56f12'},
         ],
         'enable_slow_tests': True,
         'ignore_test_result': False,
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
index f05389c915c..e1a3fda99ec 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
+++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
@@ -1,24 +1,18 @@
+change test for a warning to filterwarnings since the code may or not issue a warning depending on an arch
 see https://github.com/scipy/scipy/issues/17954 + https://github.com/scipy/scipy/pull/17975
-From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
-Date: Tue, 14 Feb 2023 17:09:13 -0500
-Subject: [PATCH 1/6] Update test_lobpcg.py
-
-test
----
- scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++----
- 1 file changed, 3 insertions(+), 4 deletions(-)
-
 diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-index afd7a106ea0..8e6de348a34 100644
+index afd7a106ea0..87f3756c37d 100644
 --- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
 +++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-@@ -255,17 +255,16 @@ def test_fiedler_large_12():
+@@ -255,17 +255,18 @@
      _check_fiedler(12, 2)
  
  
 -@pytest.mark.skipif(platform.machine() == 'aarch64',
 -                    reason="issue #15935")
-+@pytest.mark.filterwarnings("ignore:Failed at iteration")
+++@pytest.mark.filterwarnings("ignore:Failed at iteration")
+++@pytest.mark.filterwarnings("ignore:Exited at iteration")
+++@pytest.mark.filterwarnings("ignore:Exited postprocessing")
  def test_failure_to_run_iterations():
      """Check that the code exists gracefully without breaking. Issue #10974.
 +    The code may or not issue a warning, filtered out. Issue #15935, #17954.
@@ -30,156 +24,6 @@ index afd7a106ea0..8e6de348a34 100644
 -    with pytest.warns(UserWarning, match="Failed at iteration"):
 -        eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
 +    eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
-     assert np.max(eigenvalues) > 0
- 
- 
-
-From ad2054168d1eb522cc9b71eebc9ea32aa0fbd4e3 Mon Sep 17 00:00:00 2001
-From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
-Date: Tue, 14 Feb 2023 18:14:37 -0500
-Subject: [PATCH 2/6] Update test_lobpcg.py
-
-"Exited at iteration" also needs filtering out
----
- scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-index 8e6de348a34..aa3a0c29842 100644
---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-@@ -256,6 +256,7 @@ def test_fiedler_large_12():
- 
- 
- @pytest.mark.filterwarnings("ignore:Failed at iteration")
-+@pytest.mark.filterwarnings("ignore:Exited at iteration")
- def test_failure_to_run_iterations():
-     """Check that the code exists gracefully without breaking. Issue #10974.
-     The code may or not issue a warning, filtered out. Issue #15935, #17954.
-
-From 5357bcbd970cdc6ef88be5e58ff3a46d34fde61e Mon Sep 17 00:00:00 2001
-From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
-Date: Tue, 14 Feb 2023 18:34:51 -0500
-Subject: [PATCH 3/6] Update test_lobpcg.py
-
-added one more filter
-@pytest.mark.filterwarnings("ignore:Exited postprocessing")
----
- scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-index aa3a0c29842..87f3756c37d 100644
---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-@@ -257,6 +257,7 @@ def test_fiedler_large_12():
- 
- @pytest.mark.filterwarnings("ignore:Failed at iteration")
- @pytest.mark.filterwarnings("ignore:Exited at iteration")
-+@pytest.mark.filterwarnings("ignore:Exited postprocessing")
- def test_failure_to_run_iterations():
-     """Check that the code exists gracefully without breaking. Issue #10974.
-     The code may or not issue a warning, filtered out. Issue #15935, #17954.
-
-From bcad369ce894320f310c761e0136816c0a1410fb Mon Sep 17 00:00:00 2001
-From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
-Date: Wed, 15 Feb 2023 07:59:37 -0500
-Subject: [PATCH 4/6] Update test_lobpcg.py
-
-as proposed by reviewer
----
- scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++----
- 1 file changed, 3 insertions(+), 4 deletions(-)
-
-diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-index 87f3756c37d..936cc6f8db7 100644
---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-@@ -255,9 +255,6 @@ def test_fiedler_large_12():
-     _check_fiedler(12, 2)
- 
- 
--@pytest.mark.filterwarnings("ignore:Failed at iteration")
--@pytest.mark.filterwarnings("ignore:Exited at iteration")
--@pytest.mark.filterwarnings("ignore:Exited postprocessing")
- def test_failure_to_run_iterations():
-     """Check that the code exists gracefully without breaking. Issue #10974.
-     The code may or not issue a warning, filtered out. Issue #15935, #17954.
-@@ -266,7 +263,9 @@ def test_failure_to_run_iterations():
-     X = rnd.standard_normal((100, 10))
-     A = X @ X.T
-     Q = rnd.standard_normal((X.shape[0], 4))
--    eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
-+    with warnings.catch_warnings():
-+        warnings.simplefilter("ignore")
-+        eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
-     assert np.max(eigenvalues) > 0
- 
- 
-
-From bf8f497984c2056819068d8da5231c1e430659b3 Mon Sep 17 00:00:00 2001
-From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
-Date: Wed, 15 Feb 2023 10:25:29 -0500
-Subject: [PATCH 5/6] Update test_lobpcg.py
-
-import warnings added
----
- scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-index 936cc6f8db7..db87940e6a8 100644
---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-@@ -4,6 +4,7 @@
- import itertools
- import platform
- import sys
-+import warnings
- import pytest
- import numpy as np
- from numpy import ones, r_, diag
-
-From 77b9f45041bcfcb8e531b4d44c0399f103850e4d Mon Sep 17 00:00:00 2001
-From: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
-Date: Wed, 15 Feb 2023 11:51:01 -0500
-Subject: [PATCH 6/6] Update test_lobpcg.py
-
-fall back to what has passed
----
- scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-index db87940e6a8..87f3756c37d 100644
---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py
-@@ -4,7 +4,6 @@
- import itertools
- import platform
- import sys
--import warnings
- import pytest
- import numpy as np
- from numpy import ones, r_, diag
-@@ -256,6 +255,9 @@ def test_fiedler_large_12():
-     _check_fiedler(12, 2)
- 
- 
-+@pytest.mark.filterwarnings("ignore:Failed at iteration")
-+@pytest.mark.filterwarnings("ignore:Exited at iteration")
-+@pytest.mark.filterwarnings("ignore:Exited postprocessing")
- def test_failure_to_run_iterations():
-     """Check that the code exists gracefully without breaking. Issue #10974.
-     The code may or not issue a warning, filtered out. Issue #15935, #17954.
-@@ -264,9 +266,7 @@ def test_failure_to_run_iterations():
-     X = rnd.standard_normal((100, 10))
-     A = X @ X.T
-     Q = rnd.standard_normal((X.shape[0], 4))
--    with warnings.catch_warnings():
--        warnings.simplefilter("ignore")
--        eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
-+    eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12)
-     assert np.max(eigenvalues) > 0
+     assert(np.max(eigenvalues) > 0)
  
  

From 95080c97c4c5d47aacca3a156a70b3d8bd748371 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Thu, 13 Apr 2023 18:32:00 +0100
Subject: [PATCH 317/601] remove extra +

---
 .../s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb       | 2 +-
 .../s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch       | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
index ec4572d24d0..9f60a08cff4 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
+++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb
@@ -58,7 +58,7 @@ exts_list = [
             {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'},
             {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch':
              '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'},
-            {'scipy-1.10.1_fix-lobpcg-test.patch': '4940d3856d66f88af4b242dcd3b83f83a9b30da36ead73776f8d72cc17c56f12'},
+            {'scipy-1.10.1_fix-lobpcg-test.patch': 'eb4c576959108df0b1749705e64fe42e79edcf5aa8f6b4d7908f9b136d0d6648'},
         ],
         'enable_slow_tests': True,
         'ignore_test_result': False,
diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
index e1a3fda99ec..45668de46ae 100644
--- a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
+++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch
@@ -10,9 +10,9 @@ index afd7a106ea0..87f3756c37d 100644
  
 -@pytest.mark.skipif(platform.machine() == 'aarch64',
 -                    reason="issue #15935")
-++@pytest.mark.filterwarnings("ignore:Failed at iteration")
-++@pytest.mark.filterwarnings("ignore:Exited at iteration")
-++@pytest.mark.filterwarnings("ignore:Exited postprocessing")
++@pytest.mark.filterwarnings("ignore:Failed at iteration")
++@pytest.mark.filterwarnings("ignore:Exited at iteration")
++@pytest.mark.filterwarnings("ignore:Exited postprocessing")
  def test_failure_to_run_iterations():
      """Check that the code exists gracefully without breaking. Issue #10974.
 +    The code may or not issue a warning, filtered out. Issue #15935, #17954.

From 3b22c01c46bb91ce2d39a0f8f7c5df8a6b1a7def Mon Sep 17 00:00:00 2001
From: rocky_build <rocky_build@rocky7.rocky.bio.utk.edu>
Date: Thu, 13 Apr 2023 13:37:00 -0400
Subject: [PATCH 318/601] adding easyconfigs: phyx-1.3-foss-2022a.eb,
 Armadillo-11.4.3-foss-2022a.eb and patches: phyx-1.3_link_flexiblas.patch

---
 .../Armadillo/Armadillo-11.4.3-foss-2022a.eb  | 22 ++++++++
 .../easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 51 +++++++++++++++++++
 .../p/phyx/phyx-1.3_link_flexiblas.patch      | 14 +++++
 3 files changed, 87 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch

diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb
new file mode 100644
index 00000000000..261ecca60bb
--- /dev/null
+++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb
@@ -0,0 +1,22 @@
+name = 'Armadillo'
+version = '11.4.3'
+
+homepage = 'https://arma.sourceforge.net/'
+description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
+ a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
+ as well as a subset of trigonometric and statistics functions."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://sourceforge.net/projects/arma/files']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2']
+
+builddependencies = [('CMake', '3.24.3')]
+
+dependencies = [
+    ('Boost', '1.79.0'),
+    ('arpack-ng', '3.8.0'),
+]
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
new file mode 100644
index 00000000000..1418ab60d05
--- /dev/null
+++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
@@ -0,0 +1,51 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+easyblock = 'ConfigureMake'
+
+name = 'phyx'
+version = '1.3'
+
+homepage = 'https://github.com/FePhyFoFum/%(name)s'
+description = "phyx performs phylogenetics analyses on trees and sequences."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+github_account = 'FePhyFoFum'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_link_flexiblas.patch']
+checksums = [
+    {'v1.3.tar.gz': 'b09677f98f997838b39cd2724463be06d0627ddc90a7e659dc90d4e02db624eb'},
+    {'phyx-1.3_link_flexiblas.patch': 'e9dc98da0f3c5df8e5b8ac3e64c2b0f77358f61fc60a4aadce5ad790b636ebdd'},
+]
+
+builddependencies = [
+    ('Autotools', '20220317', '', ('GCCcore', '11.3.0')),
+]
+
+dependencies = [
+    ('Armadillo', '11.4.3'),
+    ('NLopt', '2.7.1'),
+]
+
+start_dir = 'src'
+
+#preconfigopts = 'autoconf && '
+preconfigopts = "autoreconf -f -i && "
+
+
+preinstallopts = 'mkdir %(installdir)s/bin && '
+
+sanity_check_paths = {
+    'files': ['bin/' + _exec for _exec in ["pxaa2cdn", "pxbdfit", "pxbdsim",
+                                           "pxboot", "pxbp", "pxcat", "pxclsq", "pxcltr", "pxcolt", "pxconsq",
+                                           "pxcontrates", "pxfqfilt", "pxlog", "pxlssq", "pxlstr", "pxmrca",
+                                           "pxmrcacut", "pxmrcaname", "pxnw", "pxrecode", "pxrevcomp",
+                                           "pxrls", "pxrlt", "pxrmk", "pxrms", "pxrmt", "pxrr", "pxs2fa", "pxs2nex",
+                                           "pxs2phy", "pxseqgen", "pxssort", "pxsstat", "pxstrec", "pxsw", "pxt2new",
+                                           "pxt2nex", "pxtcol", "pxtcomb", "pxtlate", "pxtrt", "pxtscale",
+                                           "pxvcf2fa"]],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch
new file mode 100644
index 00000000000..1b541919cf8
--- /dev/null
+++ b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch
@@ -0,0 +1,14 @@
+replace linking with lapack and blas by flexiblas
+autor: Graham Derryberry
+diff -Naur phyx-1.3.orig/src/Makefile.in phyx-1.3/src/Makefile.in
+--- phyx-1.3.orig/src/Makefile.in	2023-04-12 22:44:14.000000000 -0400
++++ phyx-1.3/src/Makefile.in	2023-04-13 09:57:34.000000000 -0400
+@@ -17,7 +17,7 @@
+ HARM := @HARM@
+ HOMP := @HOMP@
+ 
+-CPP_LIBS = -llapack -lblas -lpthread -lm
++CPP_LIBS = -lflexiblas -lpthread -lm
+ ifeq "$(HNLOPT)" "Y"
+     CPP_LIBS += -lnlopt
+ endif

From ad4a7024987d2c486de9e4edbbea0962b11df1d9 Mon Sep 17 00:00:00 2001
From: rocky_build <rocky_build@rocky7.rocky.bio.utk.edu>
Date: Thu, 13 Apr 2023 14:07:37 -0400
Subject: [PATCH 319/601] Fixing style error by removing commented out dead
 code

---
 easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
index 1418ab60d05..8eb989c720d 100644
--- a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
@@ -30,10 +30,8 @@ dependencies = [
 
 start_dir = 'src'
 
-#preconfigopts = 'autoconf && '
 preconfigopts = "autoreconf -f -i && "
 
-
 preinstallopts = 'mkdir %(installdir)s/bin && '
 
 sanity_check_paths = {

From 942ab161e81b9de042c8cc0f79589936f42a5165 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Apr 2023 09:13:07 +0200
Subject: [PATCH 320/601] adding easyconfigs: RevBayes-1.2.1-gompi-2022a.eb

---
 .../r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb  | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb
new file mode 100644
index 00000000000..525ec2e7c03
--- /dev/null
+++ b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb
@@ -0,0 +1,40 @@
+# easybuild easyconfig
+#
+# John Dey <jfdey@fredhutch.org>
+# Fred Hutchinson Cancer Research Center - Seattle Washington - US
+easyblock = 'CmdCp'
+
+name = 'RevBayes'
+version = '1.2.1'
+
+homepage = 'https://revbayes.github.io'
+description = """RevBayes provides an interactive environment for statistical computation in
+ phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in
+ evolutionary biology, particularly phylogenetics."""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://github.com/revbayes/revbayes/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['58c320ee7251a7a244aba57b471a6e695f3db8196ea4c9381bb2bc1076bcedfa']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Boost', '1.79.0'),
+]
+
+start_dir = 'projects/cmake'
+local_cmd = './build.sh -mpi true -DCMAKE_CXX_FLAGS="-pthread" -DBoost_NO_BOOST_CMAKE=ON'
+cmds_map = [('', local_cmd)]
+
+files_to_copy = [(['projects/cmake/rb-mpi'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/rb-mpi'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

From 42aed9962f7c0bb46bea6e6b5d6811d7582bb555 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Apr 2023 09:28:35 +0200
Subject: [PATCH 321/601] use CUDA variant of OpenMM 7.5.1 as dependency for
 AlphaFold 2.3.0

---
 .../AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb |  2 +-
 ...1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb | 66 +++++++++++++++++++
 2 files changed, 67 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb
index 348e3a6aaed..b37b644450f 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb
@@ -29,7 +29,7 @@ dependencies = [
     ('UCX-CUDA', '1.11.2', versionsuffix),
     ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM),
     ('NCCL', '2.10.3', versionsuffix),
-    ('OpenMM', '7.5.1', '-DeepMind-patch'),
+    ('OpenMM', '7.5.1', '%(versionsuffix)s-DeepMind-patch'),
 ]
 
 # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb
new file mode 100644
index 00000000000..335b9a7e2da
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb
@@ -0,0 +1,66 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenMM'
+version = '7.5.1'
+versionsuffix = '-CUDA-%(cudaver)s-DeepMind-patch'
+
+homepage = 'https://openmm.org'
+description = "OpenMM is a toolkit for molecular simulation."
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/openmm/openmm/archive/']
+sources = ['%(version)s.tar.gz']
+patches = [
+    ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'),
+    'OpenMM-7.5.0_fix_path_to_nvcc.patch',
+    'OpenMM-8.0.0_add_no_tree_vectorize.patch',
+]
+checksums = [
+    {'7.5.1.tar.gz': 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7'},
+    {'OpenMM-7.5.1_DeepMind.patch': '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6'},
+    {'OpenMM-7.5.0_fix_path_to_nvcc.patch': '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c'},
+    {'OpenMM-8.0.0_add_no_tree_vectorize.patch': '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd'},
+]
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+    ('Doxygen', '1.9.1'),
+]
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),
+    ('CUDA', '11.4.1', '', SYSTEM),
+    ('SWIG', '4.0.2'),
+]
+
+# Flags for CUDA-enabled build
+configopts = "-DOPENMM_BUILD_CUDA_LIB=ON"
+
+# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373
+pretestopts = " CTEST_OUTPUT_ON_FAILURE=1"
+local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)"
+runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern
+
+preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '
+preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && '
+
+# required to install the python API
+installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'],
+    'dirs': []
+}
+
+sanity_check_commands = ["python -m simtk.testInstallation"]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+    'OPENMM_INCLUDE_PATH': 'include',
+    'OPENMM_LIB_PATH': 'lib',
+}
+
+moduleclass = 'bio'

From ecaf64829b6ee050d01edfc8ea36d6db6133c1b1 Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Fri, 14 Apr 2023 10:28:32 +0000
Subject: [PATCH 322/601] Add missing binutils builddep

---
 easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb
index d0606a41e97..0354e336f08 100644
--- a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb
@@ -12,6 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 sources = [SOURCE_TAR_GZ]
 checksums = ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa']
 
+builddependencies = [('binutils', '2.38')]
+
 dependencies = [
     ('Python', '3.10.4'),
     ('Graphviz', '5.0.0'),
@@ -22,7 +24,6 @@ download_dep_fail = True
 use_pip = True
 sanity_pip_check = True
 
-
 sanity_check_commands = ["python -c 'import ruffus.graph'"]
 
 moduleclass = 'lib'

From 56d2abd327d418a81977d5720ef5f5ba7ed2cbbd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 14 Apr 2023 13:38:08 +0200
Subject: [PATCH 323/601] adding easyconfigs: Structure-2.3.4-GCC-12.2.0.eb

---
 .../s/Structure/Structure-2.3.4-GCC-12.2.0.eb | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb
new file mode 100644
index 00000000000..94412d6b87a
--- /dev/null
+++ b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb
@@ -0,0 +1,41 @@
+##
+# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia
+# Homepage:     https://staff.flinders.edu.au/research/deep-thought
+#
+# Authors::     Robert Qiao <rob.qiao@flinders.edu.au>
+# License::     Custom
+#
+# Notes::
+##
+
+easyblock = 'MakeCp'
+
+name = 'Structure'
+version = '2.3.4'
+
+homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html'
+description = """The program structure is a free software package for using multi-locus genotype data to investigate
+ population structure."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/']
+sources = [{'download_filename': 'structure_kernel_source.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['f2b72b9189a514f53e921bbdc1aa3dbaca7ac34a8467af1f972c7e4fc9c0bb37']
+
+# Add -fcommon to fix "multiple definition" errors
+prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && '
+buildopts = 'all CC="$CC" OPT="$CFLAGS"'
+
+files_to_copy = [(['structure'], 'bin')]
+
+sanity_check_commands = [
+    'structure | grep "Version %(version)s"'
+]
+
+sanity_check_paths = {
+    'files': ['bin/structure'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

From 38820779269cb4a22508388e425357726befb0cb Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Fri, 14 Apr 2023 12:40:02 +0100
Subject: [PATCH 324/601] fix typo

Co-authored-by: Adam Huffman <verdurin@users.noreply.github.com>
---
 .../p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb
index 4c7f30339f9..f0929b054cd 100644
--- a/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb
@@ -5,7 +5,7 @@ name = 'PICI-LIGGGHTS'
 version = '3.8.1'
 
 homepage = 'https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS'
-description = """UoB Postron Imaging Centre's Improved LIGGGHTS distribution with
+description = """UoB Positron Imaging Centre's Improved LIGGGHTS distribution with
  an emphasis on the Python interface."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}

From c1f46a78b297a1a37fc81164c1ccde8e27a7de5c Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 14 Apr 2023 14:30:13 +0200
Subject: [PATCH 325/601] install shared libraries for tesseract

---
 .../easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb
index fed7c2635a0..2c7b0dfdd73 100644
--- a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb
@@ -45,6 +45,8 @@ dependencies = [
 
 separate_build_dir = True
 
+configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF']
+
 postinstallcmds = [
     'rm %(builddir)s/tessdata_best-4.1.0/configs',
     'rm -rf %(builddir)s/tessdata_best-4.1.0/tessconfigs',
@@ -56,7 +58,7 @@ modextrapaths = {
 }
 
 sanity_check_paths = {
-    'files': ['bin/tesseract'],
+    'files': ['bin/tesseract', 'lib/libtesseract.a', 'lib/libtesseract.%s' % SHLIB_EXT],
     'dirs': ['share/tessdata', 'include/tesseract']
 }
 

From 64c6649fcd73c7a1ca8acbe8ce2902698fa89cbe Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 14 Apr 2023 14:31:50 +0200
Subject: [PATCH 326/601] adding easyconfigs:
 R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb

---
 .../R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb   | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..367d0c8c5f7
--- /dev/null
+++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,58 @@
+easyblock = 'Bundle'
+
+name = 'R-tesseract'
+version = '5.1.0'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://cran.r-project.org/package=tesseract'
+description = "The R extension for using tesseract"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [('pkgconf', '1.8.0')]
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('poppler', '22.12.0'),
+    ('tesseract', '5.3.0'),
+]
+
+exts_defaultclass = 'RPackage'
+
+exts_default_options = {
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz',
+}
+
+exts_list = [
+    ('askpass', '1.1', {
+        'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'],
+    }),
+    ('qpdf', '1.3.2', {
+        'checksums': ['d9c905a4879274d72de0c638f2e14737ec0a59895cbba9814e05c62b43e8e976'],
+    }),
+    ('pdftools', '3.3.3', {
+        'checksums': ['ffc0dfa5205ac3c26ee22713289784cb6b9aada6c21417d79bfd4d7f5bd5909c'],
+    }),
+    ('rappdirs', '0.3.3', {
+        'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'],
+    }),
+    ('tesseract', version, {
+        'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' +
+                          ' LIB_DIR=$EBROOTTESSERACT/lib',
+        'checksums': ['6dae7cbc1d4cf6decabb2d1c56d95b5eb6a0a4a1cbc9f9a1c274ba558b31cdfa'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'],
+    'dirs': ['askpass', 'qpdf', 'pdftools', 'rappdirs'],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'vis'

From 79a6d8a8b0c987c945010443ba4843c4dca77b16 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 14 Apr 2023 14:35:08 +0200
Subject: [PATCH 327/601] remove unneeded separate_build_dir

---
 .../easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb   | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb
index 2c7b0dfdd73..9bf893a4d12 100644
--- a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb
@@ -43,8 +43,6 @@ dependencies = [
     ('Pango', '1.50.7'),
 ]
 
-separate_build_dir = True
-
 configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF']
 
 postinstallcmds = [

From 1674aed7cfd2f191f096dd6990ae162ea3f4069a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 14 Apr 2023 15:16:51 +0200
Subject: [PATCH 328/601] adding easyconfigs: prokka-1.14.5-gompi-2022a.eb,
 Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb

---
 .../Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb    | 28 +++++++++++
 .../p/prokka/prokka-1.14.5-gompi-2022a.eb     | 50 +++++++++++++++++++
 2 files changed, 78 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb
new file mode 100644
index 00000000000..840b2a8d6fa
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'PerlModule'
+
+name = 'Bio-SearchIO-hmmer'
+version = '1.7.3'
+
+homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3'
+description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible
+with both version 2 and version 3 of the HMMER package from http://hmmer.org."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246']
+
+dependencies = [
+    ('Perl', '5.34.1'),
+    ('BioPerl', '1.7.8'),
+]
+
+options = {'modulename': 'Bio::SearchIO::hmmer3'}
+
+sanity_check_paths = {
+    'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb
new file mode 100644
index 00000000000..c1a3cfa1cd2
--- /dev/null
+++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb
@@ -0,0 +1,50 @@
+# EasyBuild easyconfig
+#
+# John Dey jfdey@fredhutch.org
+# Fred Hutchenson Cancer Research Center
+#
+# Updated: Pavel Grochal (INUITS)
+
+easyblock = 'Tarball'
+
+name = 'prokka'
+version = '1.14.5'
+
+homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml'
+description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes."
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = ['https://github.com/tseemann/prokka/archive/']
+sources = ['v%(version)s.zip']
+checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff']
+
+dependencies = [
+    ('BioPerl', '1.7.8'),
+    ('BLAST+', '2.13.0'),
+    ('Java', '11', '', SYSTEM),
+    ('Bio-SearchIO-hmmer', '1.7.3'),
+    ('parallel', '20220722'),
+    ('tbl2asn', '20220427', '-linux64', SYSTEM),
+]
+
+local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm',
+                   'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm',
+                   'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db',
+                   'prokka-make_tarball']
+
+postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'],
+    'dirs': ['bin', 'binaries', 'db',  'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'],
+}
+
+sanity_check_commands = [
+    "prokka --version",
+    "prokka --listdb",
+]
+
+modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n"
+
+moduleclass = 'bio'

From 585880c569c0dc03ea1d6206cf2cfbb83d015f2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 14 Apr 2023 15:36:26 +0200
Subject: [PATCH 329/601] adding easyconfigs: Subread-2.0.4-GCC-11.3.0.eb

---
 .../s/Subread/Subread-2.0.4-GCC-11.3.0.eb     | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb
new file mode 100644
index 00000000000..27bc601b2e9
--- /dev/null
+++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb
@@ -0,0 +1,39 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'MakeCp'
+
+name = 'Subread'
+version = '2.0.4'
+
+homepage = 'https://subread.sourceforge.net/'
+description = """High performance read alignment, quantification and mutation discovery"""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(namelower)s-%(version)s-source.tar.gz']
+checksums = ['c54b37ed83b34318d8f119b5c02fb9d0a65c811195bcc9e1745df6daf74ca2db']
+
+start_dir = 'src'
+
+prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && "
+prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && "
+
+buildopts = " -f Makefile.Linux"
+
+files_to_copy = ['bin']
+
+local_binaries_list = [
+    'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', '%(namelower)s-align', '%(namelower)s-buildindex',
+]
+sanity_check_paths = {
+    'files': ['bin/%s' % f for f in local_binaries_list],
+    'dirs': ['bin/utilities'],
+}
+
+sanity_check_commands = [
+    'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh'
+]
+
+moduleclass = 'bio'

From 84c717f657e2047dddb11fc6ae212a09b4f663c7 Mon Sep 17 00:00:00 2001
From: jfgrimm <jasper.grimm@york.ac.uk>
Date: Fri, 14 Apr 2023 14:38:49 +0100
Subject: [PATCH 330/601] let EasyBuild map toolchains automatically

---
 .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb        | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
index 8666c0f0dc9..6bb64936f1e 100644
--- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
@@ -7,8 +7,6 @@ homepage = 'https://easybuild.io/'
 description = """Python distribution with a number of widely used 
 extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """
 
-local_gccver = '11.3.0'
-
 toolchain = {'name': 'foss', 'version': '2022a'}
 toolchainopts = {'pic': True, 'lowopt': True}
 
@@ -16,7 +14,7 @@ dependencies = [
     ('Python', version),
     ('SciPy-bundle', '2022.05'),
     ('matplotlib', '3.5.2'),
-    ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)),
+    ('JupyterLab', '3.5.0'),
 ]
 
 sanity_check_paths = {

From 5c29f147dbef75ac8e6af824c91ed75667698972 Mon Sep 17 00:00:00 2001
From: jfgrimm <jasper.grimm@york.ac.uk>
Date: Fri, 14 Apr 2023 14:39:23 +0100
Subject: [PATCH 331/601] remove sanity check, and add moduleclass

---
 .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb       | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
index 6bb64936f1e..0d2db0765c9 100644
--- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb
@@ -17,7 +17,4 @@ dependencies = [
     ('JupyterLab', '3.5.0'),
 ]
 
-sanity_check_paths = {
-    'files': [],
-    'dirs': ["easybuild/"],
-}
+moduleclass = 'lang'

From 315b36740f23596f2439ea7eb8a0784a9781773c Mon Sep 17 00:00:00 2001
From: jfgrimm <jasper.grimm@york.ac.uk>
Date: Fri, 14 Apr 2023 14:41:53 +0100
Subject: [PATCH 332/601] add Python-bundle to bundles_whitelist in
 test_pr_sanity_check_paths

---
 test/easyconfigs/easyconfigs.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index 9e2523ae1b9..40c597ba675 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -1130,8 +1130,9 @@ def test_pr_sanity_check_paths(self):
                      'PythonBundle', 'PythonPackage', 'Toolchain']
         # Bundles of dependencies without files of their own
         # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore,
-        # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co
-        bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm']
+        # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co,
+        # Python-bundle: Python + SciPy-bundle + matplotlib + JupyterLab
+        bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'Python-bundle', 'ROCm']
 
         failing_checks = []
 

From 7fdbaa70628e4428ca99f75a2b1406dddd3cb090 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 14 Apr 2023 15:55:12 +0200
Subject: [PATCH 333/601] adding easyconfigs: Kraken2-2.1.2-gompi-2022a.eb

---
 .../k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb    | 62 +++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb
new file mode 100644
index 00000000000..78064ba7f3e
--- /dev/null
+++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb
@@ -0,0 +1,62 @@
+easyblock = 'PackedBinary'
+
+name = 'Kraken2'
+version = '2.1.2'
+
+homepage = 'https://github.com/DerrickWood/kraken2/wiki'
+description = """Kraken is a system for assigning taxonomic labels to short DNA sequences,
+ usually obtained through metagenomic studies. Previous attempts by other
+ bioinformatics software to accomplish this task have often used sequence
+ alignment or machine learning techniques that were quite slow, leading to
+ the development of less sensitive but much faster abundance estimation
+ programs. Kraken aims to achieve high sensitivity and high speed by
+ utilizing exact alignments of k-mers and a novel classification algorithm."""
+
+# part is compiled with $CXX, the rest is in Perl
+toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchainopts = {'openmp': True, 'cstd': 'c++11'}
+
+github_account = 'DerrickWood'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    '%(name)s-2.1.1_fix_installation_for_easybuild.patch',
+    '%(name)s-%(version)s_fix_ncbi_https_server.patch',
+]
+checksums = [
+    'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3',  # v2.1.2.tar.gz
+    # Kraken2-2.1.1_fix_installation_for_easybuild.patch
+    '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11',
+    '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116',  # Kraken2-2.1.2_fix_ncbi_https_server.patch
+]
+
+dependencies = [
+    ('Perl', '5.34.1'),
+    ('BLAST+', '2.13.0'),
+    ('wget', '1.21.3'),
+]
+
+install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && '
+install_cmd += './install_kraken2.sh %(installdir)s/bin'
+
+# Kraken2 databases can be downloaded from https://benlangmead.github.io/aws-indexes/k2
+# or built as described in https://github.com/DerrickWood/kraken2/wiki/Manual#kraken-2-databases
+# The following commands will build and install the standard databases (100GB) in local_db_path
+# local_db_path = '%(installdir)s/db'
+# postinstallcmds = [
+#     'mkdir %s' % local_db_path,
+#     'cd %%(installdir)s/bin && ./kraken2-build --standard --threads %%(parallel)s --db %s' % local_db_path,
+# ]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in [
+        '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh',
+        'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl',
+        'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh',
+        'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm',
+        'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl',
+        'scan_fasta_file.pl']],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

From db2cfd72de79fe98b62ea75d5740d864607b2ac4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 14 Apr 2023 16:03:10 +0200
Subject: [PATCH 334/601] add a few sanity check commands

---
 .../easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb    | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb
index 78064ba7f3e..9ed7324537c 100644
--- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb
+++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb
@@ -59,4 +59,12 @@ sanity_check_paths = {
     'dirs': [],
 }
 
+sanity_check_commands = [
+    'kraken2 --help',
+    'kraken2-build --help',
+    'kraken2-inspect --help',
+    'build_db -h',
+    'classify -h',
+]
+
 moduleclass = 'bio'

From d129d03285cc090a2d55f061146aee6fe65c72b5 Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <viktor.rehnberg@gmail.com>
Date: Fri, 14 Apr 2023 16:30:18 +0200
Subject: [PATCH 335/601] PyTorch-1.12.1-foss-2022a-CUDA-11.7.0 fix flaky test
 optim test

---
 .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb  |   3 +
 ....1_use-predefined-data-in-test-optim.patch | 132 ++++++++++++++++++
 2 files changed, 135 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
index 528fb671557..a62ed5dddbe 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -44,6 +44,7 @@ patches = [
     'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
     'PyTorch-1.12.1_skip-failing-grad-test.patch',
     'PyTorch-1.12.1_skip-test_round_robin.patch',
+    'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch',
 ]
 checksums = [
     '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
@@ -99,6 +100,8 @@ checksums = [
     '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
     # PyTorch-1.12.1_skip-test_round_robin.patch
     '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349',
+    # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
+    'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054',
 ]
 
 osdependencies = [OS_PKG_IBVERBS_DEV]
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
new file mode 100644
index 00000000000..5dc393c17fd
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
@@ -0,0 +1,132 @@
+The test test_optim.test_nadam has high error rate, this let's the test use
+predefined data instead to be more stable. See
+https://github.com/pytorch/pytorch/issues/98414
+
+Viktor Rehnberg
+diff --git a/test/test_optim.py b/test/test_optim.py
+index 6d587b4b352..c8ec9db87e1 100644
+--- a/test/test_optim.py
++++ b/test/test_optim.py
+@@ -244,8 +244,14 @@ class TestOptim(TestCase):
+             return set(k for k in obj.__dict__ if not k.startswith('_'))
+         self.assertEqual(getPublicAttr(optimizer), getPublicAttr(deepcopy(optimizer)))
+ 
+-    def _test_basic_cases(self, constructor, scheduler_constructors=None,
+-                          ignore_multidevice=False, constructor_accepts_maximize=False):
++    def _test_basic_cases(
++        self,
++        constructor,
++        scheduler_constructors=None,
++        ignore_multidevice=False,
++        constructor_accepts_maximize=False,
++        use_predefined_data=False,
++    ):
+         if scheduler_constructors is None:
+             scheduler_constructors = []
+ 
+@@ -254,26 +260,60 @@ class TestOptim(TestCase):
+                 return lambda weight, bias: constructor(weight, bias, maximize)
+             return constructor
+ 
++        def make_weight_tensor():
++            if use_predefined_data:
++                return torch.Tensor([
++                    [ 0.6390, -0.5524, -0.1877, -1.1132,  0.3412],
++                    [-0.6489, -0.6220, -1.2537, -0.0966,  0.5481],
++                    [-0.6923,  0.5768, -0.9141,  1.9410,  1.0036],
++                    [ 0.5842,  1.1618, -0.1871,  1.0344,  0.5668],
++                    [ 0.2123,  2.3076,  0.7522, -0.7059,  1.3849],
++                    [-0.1537,  0.5159, -1.2004,  0.2017, -0.0903],
++                    [ 0.9434, -0.7030,  0.0618, -1.2951,  1.7721],
++                    [ 0.5890, -1.0763, -1.2541, -0.8403, -0.4343],
++                    [-0.2065, -0.6883,  0.8464, -0.7792,  0.6750],
++                    [-1.6577,  0.4532,  0.0791,  0.2243,  0.1148],
++                ])
++            else:
++                return torch.randn(10, 5)
++
++        def make_bias_tensor():
++            if use_predefined_data:
++                return torch.Tensor([
++                    -2.4031, -0.9295, -1.0762,  0.4600, -1.8620, -0.6234,  0.1999, -0.0612, 0.8319, -1.6673,
++                ])
++            else:
++                return torch.randn(10)
++
++        def make_input_tensor():
++            if use_predefined_data:
++                return torch.Tensor([1.1119, -0.4309, -0.7759, -0.0659,  0.4746])
++            else:
++                return torch.randn(5)
++
++        def make_non_contiguous(tensor):
++            return torch.stack([tensor, tensor]).view(*tensor.size(), 2)[..., 0]
++
+         for maximize in (True, False):
+             self._test_state_dict(
+-                torch.randn(10, 5),
+-                torch.randn(10),
+-                torch.randn(5),
++                make_weight_tensor(),
++                make_bias_tensor(),
++                make_input_tensor(),
+                 make_two_arg_constructor(constructor, maximize),
+             )
+         self._test_basic_cases_template(
+-            torch.randn(10, 5),
+-            torch.randn(10),
+-            torch.randn(5),
++            make_weight_tensor(),
++            make_bias_tensor(),
++            make_input_tensor(),
+             constructor,
+             scheduler_constructors,
+             constructor_accepts_maximize,
+         )
+         # non-contiguous parameters
+         self._test_basic_cases_template(
+-            torch.randn(10, 5, 2)[..., 0],
+-            torch.randn(10, 2)[..., 0],
+-            torch.randn(5),
++            make_non_contiguous(make_weight_tensor()),
++            make_non_contiguous(make_bias_tensor()),
++            make_input_tensor(),
+             constructor,
+             scheduler_constructors,
+             constructor_accepts_maximize,
+@@ -282,9 +322,9 @@ class TestOptim(TestCase):
+         if not torch.cuda.is_available():
+             return
+         self._test_basic_cases_template(
+-            torch.randn(10, 5).cuda(),
+-            torch.randn(10).cuda(),
+-            torch.randn(5).cuda(),
++            make_weight_tensor().cuda(),
++            make_bias_tensor().cuda(),
++            make_input_tensor().cuda(),
+             constructor,
+             scheduler_constructors,
+             constructor_accepts_maximize,
+@@ -293,9 +333,9 @@ class TestOptim(TestCase):
+         if not torch.cuda.device_count() > 1 or ignore_multidevice:
+             return
+         self._test_basic_cases_template(
+-            torch.randn(10, 5).cuda(0),
+-            torch.randn(10).cuda(1),
+-            torch.randn(5).cuda(0),
++            make_weight_tensor().cuda(0),
++            make_bias_tensor().cuda(1),
++            make_input_tensor().cuda(0),
+             constructor,
+             scheduler_constructors,
+             constructor_accepts_maximize,
+@@ -668,7 +708,8 @@ class TestOptim(TestCase):
+             self._test_basic_cases(
+                 lambda weight, bias: optimizer(
+                     self._build_params_dict(weight, bias, lr=1e-2),
+-                    lr=1e-3)
++                    lr=1e-3),
++                use_predefined_data=True,
+             )
+             self._test_basic_cases(
+                 lambda weight, bias: optimizer([weight, bias], lr=1e-3, weight_decay=0.1, momentum_decay=6e-3)

From 1404041f71da1741c3c657ddd4325f289870d746 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Apr 2023 18:48:35 +0200
Subject: [PATCH 336/601] add tvem extension to R 4.2.1

---
 easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
index 2efbf9482f0..67f669fec01 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
@@ -3478,6 +3478,9 @@ exts_list = [
     ('ppcor', '1.1', {
         'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
     }),
+    ('tvem', '1.3.1', {
+        'checksums': ['931085e210891744df64288ce174dface7a68bdb6b21a5883a9d83bb66a132c3'],
+    }),
 ]
 
 moduleclass = 'lang'

From 92b4203a7392059ecbc156ec966e19171bda0047 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 14 Apr 2023 19:52:36 +0200
Subject: [PATCH 337/601] Update
 easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb

---
 easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
index 8eb989c720d..ba5ddd69573 100644
--- a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb
@@ -20,7 +20,7 @@ checksums = [
 ]
 
 builddependencies = [
-    ('Autotools', '20220317', '', ('GCCcore', '11.3.0')),
+    ('Autotools', '20220317'),
 ]
 
 dependencies = [

From ddf44bbe195f35283d9147847609643957566a2d Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 15 Apr 2023 12:59:43 +0100
Subject: [PATCH 338/601] fix flaky test optim test PyTorch 1.12.1 foss/2022a

---
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
index c31da630572..415463c968a 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
@@ -41,6 +41,7 @@ patches = [
     'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
     'PyTorch-1.12.1_skip-failing-grad-test.patch',
     'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch',
+    'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch',
 ]
 checksums = [
     '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
@@ -92,6 +93,8 @@ checksums = [
     '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
     # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch
     '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d',
+    # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
+    'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054',
 ]
 
 osdependencies = [OS_PKG_IBVERBS_DEV]

From 1ea0fea83eb69d1c838ce6b570c0dff055362266 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 15 Apr 2023 13:00:16 +0100
Subject: [PATCH 339/601] fix flaky test optim test PyTorch 1.12.1 foss/2021b

---
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
index 7c58b58e5fd..45b84bdea56 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
@@ -41,6 +41,7 @@ patches = [
     'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
     'PyTorch-1.12.1_skip-failing-grad-test.patch',
     'PyTorch-1.12.1_skip-test_round_robin.patch',
+    'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch',
 ]
 checksums = [
     '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
@@ -92,6 +93,8 @@ checksums = [
     '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
     # PyTorch-1.12.1_skip-test_round_robin.patch
     '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349',
+    # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
+    'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054',
 ]
 
 osdependencies = [OS_PKG_IBVERBS_DEV]

From 5fe4aa37d3eb9b6fbd5802f0a8b567abd2f5974a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Apr 2023 15:49:57 +0200
Subject: [PATCH 340/601] adding easyconfigs: Casanovo-3.3.0-foss-2022a.eb

---
 .../c/Casanovo/Casanovo-3.3.0-foss-2022a.eb   | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb
new file mode 100644
index 00000000000..8318aafc346
--- /dev/null
+++ b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb
@@ -0,0 +1,69 @@
+easyblock = 'PythonBundle'
+
+name = 'Casanovo'
+version = '3.3.0'
+
+homepage = 'https://casanovo.readthedocs.io'
+description = "De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+use_pip = True
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+    ('h5py', '3.7.0'),
+    ('lxml', '4.9.1'),
+    ('einops', '0.4.1'),
+    ('PyTorch', '1.12.0'),
+    ('PyTorch-Lightning', '1.8.4'),
+    ('scikit-learn', '1.1.2'),
+    ('numba', '0.56.4'),
+    ('tensorboard', '2.10.0'),
+]
+
+exts_list = [
+    ('pyteomics', '4.5.6', {
+        'checksums': ['8c6e79068f18d853218967a312c22861422df69fdcf62499a258526f687b126f'],
+    }),
+    ('depthcharge-ms', '0.1.0', {
+        'checksums': ['237f8e70fd237fdc945882e981170321ac7da2638ba24b52f72dad9ff2262096'],
+        'modulename': 'depthcharge',
+    }),
+    ('natsort', '8.3.1', {
+        'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'],
+    }),
+    ('PyGithub', '1.58.1', {
+        'checksums': ['7d528b4ad92bc13122129fafd444ce3d04c47d2d801f6446b6e6ee2d410235b3'],
+        'modulename': 'github',
+    }),
+    ('Deprecated', '1.2.13', {
+        'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'],
+    }),
+    ('fastobo', '0.12.2', {
+        'checksums': ['2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e'],
+    }),
+    ('lark', '1.1.5', {
+        'checksums': ['4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d'],
+    }),
+    ('spectrum-utils', '0.4.1', {
+        'sources': ['spectrum_utils-%(version)s.tar.gz'],
+        'checksums': ['c4f1c80de8144fb8d6fc276968ef4d5e896dad03bb8a9316f69c73ee82affd85'],
+    }),
+    ('casanovo', version, {
+        'checksums': ['d9358c64a549d00f0568ebef65d5500ad63041e9ea2ebd348a7e650c8177ff81'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/casanovo'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["casanovo --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 11630a829321c17b4d84d9c04648a15b51c7e6be Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Apr 2023 15:50:21 +0200
Subject: [PATCH 341/601] adding easyconfigs:
 Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb

---
 .../Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb  | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..13264c0021f
--- /dev/null
+++ b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,71 @@
+easyblock = 'PythonBundle'
+
+name = 'Casanovo'
+version = '3.3.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://casanovo.readthedocs.io'
+description = "De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+use_pip = True
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('matplotlib', '3.5.2'),
+    ('h5py', '3.7.0'),
+    ('lxml', '4.9.1'),
+    ('einops', '0.4.1'),
+    ('PyTorch', '1.12.0', versionsuffix),
+    ('PyTorch-Lightning', '1.8.4', versionsuffix),
+    ('scikit-learn', '1.1.2'),
+    ('numba', '0.56.4', versionsuffix),
+    ('tensorboard', '2.10.0'),
+]
+
+exts_list = [
+    ('pyteomics', '4.5.6', {
+        'checksums': ['8c6e79068f18d853218967a312c22861422df69fdcf62499a258526f687b126f'],
+    }),
+    ('depthcharge-ms', '0.1.0', {
+        'checksums': ['237f8e70fd237fdc945882e981170321ac7da2638ba24b52f72dad9ff2262096'],
+        'modulename': 'depthcharge',
+    }),
+    ('natsort', '8.3.1', {
+        'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'],
+    }),
+    ('PyGithub', '1.58.1', {
+        'checksums': ['7d528b4ad92bc13122129fafd444ce3d04c47d2d801f6446b6e6ee2d410235b3'],
+        'modulename': 'github',
+    }),
+    ('Deprecated', '1.2.13', {
+        'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'],
+    }),
+    ('fastobo', '0.12.2', {
+        'checksums': ['2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e'],
+    }),
+    ('lark', '1.1.5', {
+        'checksums': ['4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d'],
+    }),
+    ('spectrum-utils', '0.4.1', {
+        'sources': ['spectrum_utils-%(version)s.tar.gz'],
+        'checksums': ['c4f1c80de8144fb8d6fc276968ef4d5e896dad03bb8a9316f69c73ee82affd85'],
+    }),
+    ('casanovo', version, {
+        'checksums': ['d9358c64a549d00f0568ebef65d5500ad63041e9ea2ebd348a7e650c8177ff81'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/casanovo'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["casanovo --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

From 7164894a61c46ae3b159e7f9873c314625b7c9b1 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 15 Apr 2023 18:05:11 +0100
Subject: [PATCH 342/601] revert use predefined data in test option for PyTorch
 1.12.1

---
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb   | 3 ---
 .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb         | 3 ---
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb   | 3 ---
 3 files changed, 9 deletions(-)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
index 45b84bdea56..7c58b58e5fd 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
@@ -41,7 +41,6 @@ patches = [
     'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
     'PyTorch-1.12.1_skip-failing-grad-test.patch',
     'PyTorch-1.12.1_skip-test_round_robin.patch',
-    'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch',
 ]
 checksums = [
     '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
@@ -93,8 +92,6 @@ checksums = [
     '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
     # PyTorch-1.12.1_skip-test_round_robin.patch
     '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349',
-    # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
-    'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054',
 ]
 
 osdependencies = [OS_PKG_IBVERBS_DEV]
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
index a62ed5dddbe..528fb671557 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -44,7 +44,6 @@ patches = [
     'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
     'PyTorch-1.12.1_skip-failing-grad-test.patch',
     'PyTorch-1.12.1_skip-test_round_robin.patch',
-    'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch',
 ]
 checksums = [
     '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
@@ -100,8 +99,6 @@ checksums = [
     '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
     # PyTorch-1.12.1_skip-test_round_robin.patch
     '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349',
-    # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
-    'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054',
 ]
 
 osdependencies = [OS_PKG_IBVERBS_DEV]
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
index 415463c968a..c31da630572 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
@@ -41,7 +41,6 @@ patches = [
     'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch',
     'PyTorch-1.12.1_skip-failing-grad-test.patch',
     'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch',
-    'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch',
 ]
 checksums = [
     '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb',  # pytorch-v1.12.1.tar.gz
@@ -93,8 +92,6 @@ checksums = [
     '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc',  # PyTorch-1.12.1_skip-failing-grad-test.patch
     # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch
     '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d',
-    # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch
-    'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054',
 ]
 
 osdependencies = [OS_PKG_IBVERBS_DEV]

From 85ec3bf10f46489ced77fbf73aa07d6c32b8eaae Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Sun, 16 Apr 2023 17:15:21 +0200
Subject: [PATCH 343/601] update recent R easyconfigs with additional R
 packages

---
 .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb     | 53 ++++++++++++++++---
 .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb     | 42 +++++++++++++++
 2 files changed, 88 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
index 67f669fec01..34241cc8cdc 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
@@ -1798,8 +1798,8 @@ exts_list = [
     ('HWxtest', '1.1.9', {
         'patches': ['HWxtest-1.1.9_add-fcommon.patch'],
         'checksums': [
-            'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6',  # HWxtest_1.1.9.tar.gz
-            '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451',  # HWxtest-1.1.9_add-fcommon.patch
+            {'HWxtest_1.1.9.tar.gz': 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6'},
+            {'HWxtest-1.1.9_add-fcommon.patch': '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451'},
         ],
     }),
     ('diveRsity', '1.9.90', {
@@ -2322,9 +2322,9 @@ exts_list = [
         # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC
         'preinstallopts': 'LIQUIDSVM_TARGET="empty"',
         'checksums': [
-            '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba',  # liquidSVM_1.2.4.tar.gz
-            # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch
-            '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8',
+            {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'},
+            {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch':
+             '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'},
         ],
     }),
     ('oddsratio', '2.0.1', {
@@ -3478,8 +3478,47 @@ exts_list = [
     ('ppcor', '1.1', {
         'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
     }),
-    ('tvem', '1.3.1', {
-        'checksums': ['931085e210891744df64288ce174dface7a68bdb6b21a5883a9d83bb66a132c3'],
+    ('berryFunctions', '1.22.0', {
+        'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'],
+    }),
+    ('cld2', '1.2.4', {
+        'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'],
+    }),
+    ('crfsuite', '0.4.1', {
+        'checksums': ['be4f8e7773caa2e3ceac7e35d47ef323f6b121d2b2da1e3b90b4e3b4fc7da46e'],
+    }),
+    ('doc2vec', '0.2.0', {
+        'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'],
+    }),
+    ('fastDummies', '1.6.3', {
+        'checksums': ['bd3934fe19d7dff2723438bbb7b89334118143f8ce151d98477ae964ee5d81df'],
+    }),
+    ('quanteda', '3.2.3', {
+        'checksums': ['f34b0e89ad7795eed0d624fb57a9fb924175a03df0c23fc1f71eefe6a14d93ae'],
+    }),
+    ('rlist', '0.4.6.2', {
+        'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'],
+    }),
+    ('ISOweek', '0.6-2', {
+        'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'],
+    }),
+    ('sentometrics', '1.0.0', {
+        'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'],
+    }),
+    ('tau', '0.0-24', {
+        'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'],
+    }),
+    ('textcat', '1.0-8', {
+        'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'],
+    }),
+    ('textplot', '0.2.2', {
+        'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'],
+    }),
+    ('udpipe', '0.8.11', {
+        'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'],
+    }),
+    ('word2vec', '0.3.4', {
+        'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'],
     }),
 ]
 
diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
index f89a16e5c6d..e8a09bc8b64 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
@@ -3549,6 +3549,48 @@ exts_list = [
     ('ppcor', '1.1', {
         'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
     }),
+    ('berryFunctions', '1.22.0', {
+        'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'],
+    }),
+    ('cld2', '1.2.4', {
+        'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'],
+    }),
+    ('crfsuite', '0.4.1', {
+        'checksums': ['be4f8e7773caa2e3ceac7e35d47ef323f6b121d2b2da1e3b90b4e3b4fc7da46e'],
+    }),
+    ('doc2vec', '0.2.0', {
+        'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'],
+    }),
+    ('fastDummies', '1.6.3', {
+        'checksums': ['bd3934fe19d7dff2723438bbb7b89334118143f8ce151d98477ae964ee5d81df'],
+    }),
+    ('quanteda', '3.3.0', {
+        'checksums': ['03256faf63455d16d643349a34b068d0bf69506a0e952b99ab2391e6423663a5'],
+    }),
+    ('rlist', '0.4.6.2', {
+        'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'],
+    }),
+    ('ISOweek', '0.6-2', {
+        'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'],
+    }),
+    ('sentometrics', '1.0.0', {
+        'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'],
+    }),
+    ('tau', '0.0-24', {
+        'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'],
+    }),
+    ('textcat', '1.0-8', {
+        'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'],
+    }),
+    ('textplot', '0.2.2', {
+        'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'],
+    }),
+    ('udpipe', '0.8.11', {
+        'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'],
+    }),
+    ('word2vec', '0.3.4', {
+        'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'],
+    }),
 ]
 
 moduleclass = 'lang'

From 2a918696a3f5eb48a02e923699df0dbe5bdd6242 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Sun, 16 Apr 2023 17:26:34 +0200
Subject: [PATCH 344/601] re-add tvem

---
 easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
index 34241cc8cdc..c0a40a9552d 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
@@ -3478,6 +3478,9 @@ exts_list = [
     ('ppcor', '1.1', {
         'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'],
     }),
+    ('tvem', '1.3.1', {
+        'checksums': ['931085e210891744df64288ce174dface7a68bdb6b21a5883a9d83bb66a132c3'],
+    }),
     ('berryFunctions', '1.22.0', {
         'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'],
     }),

From ddfc056fb45612e645daab725be78b92b75073e2 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Sun, 16 Apr 2023 17:51:32 +0200
Subject: [PATCH 345/601] adding easyconfigs: RPostgreSQL-0.7-5-foss-2022a.eb

---
 .../RPostgreSQL-0.7-5-foss-2022a.eb           | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb

diff --git a/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb b/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb
new file mode 100644
index 00000000000..88f4b40198b
--- /dev/null
+++ b/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb
@@ -0,0 +1,48 @@
+easyblock = 'Bundle'
+
+name = 'RPostgreSQL'
+version = '0.7-5'
+
+homepage = 'https://cran.r-project.org/package=tesseract'
+description = """
+Database interface and 'PostgreSQL' driver for 'R'. This package provides a
+Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL'
+database systems."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('pkgconf', '1.8.0'),
+    ('Autotools', '20220317'),
+]
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('PostgreSQL', '14.4'),
+]
+
+exts_defaultclass = 'RPackage'
+
+exts_default_options = {
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz',
+}
+
+exts_list = [
+    (name, version, {
+        'checksums': ['6b5401ee55bd948ae7bc84520d789ceb422533a7d5e5bd6e10e3b54447f29fa1'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['RPostgreSQL/libs/RPostgreSQL.%s' % SHLIB_EXT, 'RPostgreSQL/R/RPostgreSQL'],
+    'dirs': [],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'data'

From 9b5e8a17067589c8d224cc286beba3a390bc3280 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 17 Apr 2023 09:27:05 +0200
Subject: [PATCH 346/601] adding easyconfigs: AlphaFold-2.3.1-foss-2022a.eb,
 OpenMM-8.0.0-foss-2022a.eb

---
 .../a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb | 159 ++++++++++++++++++
 .../o/OpenMM/OpenMM-8.0.0-foss-2022a.eb       |  60 +++++++
 2 files changed, 219 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb
new file mode 100644
index 00000000000..77990ac93a2
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb
@@ -0,0 +1,159 @@
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold'
+version = '2.3.1'
+
+homepage = 'https://deepmind.com/research/case-studies/alphafold'
+description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    # required for installing dm-tree
+    ('Bazel', '5.1.1'),
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('TensorFlow', '2.11.0'),
+    ('Biopython', '1.79'),
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.3.2'),
+    ('Kalign', '3.3.5'),
+    ('jax', '0.3.25'),  # also provides absl-py
+    ('OpenMM', '8.0.0'),
+]
+
+# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
+# see docker/Dockerfile in AlphaFold repository
+local_scp_commit = '7102c6'
+
+components = [
+    (name, version, {
+        'easyblock': 'PythonPackage',
+        'source_urls': [
+            'https://github.com/deepmind/alphafold/archive/refs/tags/',
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [
+            {
+                'download_filename': 'v%(version)s.tar.gz',
+                'filename': SOURCE_TAR_GZ,
+            },
+            {
+                'download_filename': 'stereo_chemical_props.txt',
+                'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+                'extract_cmd': "cp %s .",
+            },
+        ],
+        'patches': [
+            'AlphaFold-2.0.0_fix-packages.patch',
+            'AlphaFold-2.3.0_data-dep-paths.patch',
+            'AlphaFold-2.0.0_n-cpu.patch',
+            'AlphaFold-2.1.0_fix-scp-path.patch',
+            'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+            'AlphaFold-2.3.1_use_openmm_7.7.0.patch',
+        ],
+        'checksums': [
+            '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a',  # v2.3.1.tar.gz
+            '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
+            '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db',  # AlphaFold-2.0.0_fix-packages.patch
+            '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0',  # AlphaFold-2.3.0_data-dep-paths.patch
+            'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',  # AlphaFold-2.0.0_n-cpu.patch
+            '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f',  # AlphaFold-2.1.0_fix-scp-path.patch
+            '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac',  # AlphaFold-2.0.1_setup_rm_tfcpu.patch
+            # AlphaFold-2.3.1_use_openmm_7.7.0.patch
+            'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec',
+
+        ],
+        'start_dir': 'alphafold-%(version)s',
+        'use_pip': True,
+    }),
+]
+
+use_pip = True
+
+exts_list = [
+    ('PDBFixer', '1.8.1', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'],
+    }),
+    ('toolz', '0.12.0', {
+        'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
+    }),
+    ('chex', '0.1.6', {
+        'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'],
+    }),
+    ('tabulate', '0.9.0', {
+        'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'],
+    }),
+    ('jmp', '0.0.4', {
+        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+    }),
+    ('dm-haiku', '0.0.9', {
+        'modulename': 'haiku',
+        'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'],
+    }),
+    ('dm-tree', '0.1.8', {
+        'modulename': 'tree',
+        'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'],
+    }),
+    ('websocket-client', '1.5.1', {
+        'modulename': 'websocket',
+        'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'],
+    }),
+    ('docker', '6.0.1', {
+        'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'],
+    }),
+    ('immutabledict', '2.2.3', {
+        'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    # run_alphafold.py script is missing a shebang...
+    "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
+    "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py",
+    "chmod a+x %(installdir)s/bin/run_alphafold*.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/",
+    "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
+    # run tests for run_alphafold.py script;
+    # shouldn't do this in sanity check to avoid breaking use of --module-only
+    "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
+    "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py",
+]
+
+sanity_check_paths = {
+    'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
+}
+
+sanity_check_commands = [
+    "pdbfixer --help",
+    "python -m openmm.testInstallation",
+    "python -c 'import alphafold'",
+    "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
+]
+
+sanity_pip_check = True
+
+modextravars = {
+    'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-%(version)s',
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
new file mode 100644
index 00000000000..47d3bdbfaf5
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb
@@ -0,0 +1,60 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+# Update to 7.5.1
+# J. Sassmannshausen / GSTT
+
+easyblock = 'CMakeMake'
+
+name = 'OpenMM'
+version = '8.0.0'
+
+homepage = 'https://openmm.org'
+description = "OpenMM is a toolkit for molecular simulation."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'opt': True}
+
+source_urls = ['https://github.com/openmm/openmm/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('Doxygen', '1.9.4'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('SWIG', '4.0.2'),
+]
+
+pretestopts = " CTEST_OUTPUT_ON_FAILURE=1"
+local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)"
+runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern
+
+preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && '
+preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && '
+
+# required to install the python API
+installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['lib/libOpenMM.%s' % SHLIB_EXT],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+sanity_check_commands = [
+    "python -c 'import simtk.openmm'",
+    "python -m openmm.testInstallation",
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg',
+    'OPENMM_INCLUDE_PATH': 'include',
+    'OPENMM_LIB_PATH': 'lib',
+}
+
+moduleclass = 'bio'

From 6cf20bad67d360d2c60fea43a7e1b3a06b0e8116 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 17 Apr 2023 09:49:12 +0200
Subject: [PATCH 347/601] comment out ALPHAFOLD_DATA_DIR in
 AlphaFold-2.3.1-foss-2022a.eb

---
 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb
index 77990ac93a2..565504238bb 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb
@@ -153,7 +153,7 @@ sanity_check_commands = [
 sanity_pip_check = True
 
 modextravars = {
-    'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-%(version)s',
+    # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs',  # please adapt
 }
 
 moduleclass = 'bio'

From 8d95a7d96fd1ed37c1752c5830ee327c1a9ed95d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 17 Apr 2023 09:59:09 +0200
Subject: [PATCH 348/601] upgrade dependency on Libint to v2.7.2 and PLUMED to
 v2.8.1 of CP2K v9.1 and v2022.1

---
 .../c/CP2K/CP2K-2022.1-foss-2022a.eb          |  4 +-
 .../easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb |  4 +-
 .../Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb    | 52 ----------------
 .../p/PLUMED/PLUMED-2.8.0-foss-2022a.eb       | 60 -------------------
 4 files changed, 4 insertions(+), 116 deletions(-)
 delete mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb
 delete mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb
index 3521d55a090..a979cbf28d2 100644
--- a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb
@@ -19,11 +19,11 @@ checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b']
 
 #                https://github.com/cp2k/cp2k/releases/download/v2022.1/cp2k-2022.1.tar.bz2
 dependencies = [
-    ('Libint', '2.6.0', '-lmax-6-cp2k'),
+    ('Libint', '2.7.2', '-lmax-6-cp2k'),
     ('libxc', '5.2.3'),
     ('libxsmm', '1.17'),
     ('FFTW', '3.3.10'),
-    ('PLUMED', '2.8.0'),
+    ('PLUMED', '2.8.1'),
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb
index b2e72836ed6..67b7353f347 100644
--- a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb
@@ -18,11 +18,11 @@ sources = [SOURCELOWER_TAR_BZ2]
 checksums = ['fedb4c684a98ad857cd49b69a3ae51a73f85a9c36e9cb63e3b02320c74454ce6']
 
 dependencies = [
-    ('Libint', '2.6.0', '-lmax-6-cp2k'),
+    ('Libint', '2.7.2', '-lmax-6-cp2k'),
     ('libxc', '5.2.3'),
     ('libxsmm', '1.17'),
     ('FFTW', '3.3.10'),
-    ('PLUMED', '2.8.0'),
+    ('PLUMED', '2.8.1'),
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb
deleted file mode 100644
index a992dd7921d..00000000000
--- a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb
+++ /dev/null
@@ -1,52 +0,0 @@
-##
-# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
-##
-name = 'Libint'
-version = '2.6.0'
-local_lmax = 6
-# custom configuration, to be used as dependency for CP2K
-versionsuffix = '-lmax-%s-cp2k' % local_lmax
-
-homepage = 'https://github.com/evaleev/libint'
-description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
- matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory."""
-
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
-toolchainopts = {'pic': True, 'cstd': 'c++11'}
-
-source_urls = ['https://github.com/evaleev/libint/archive']
-sources = ['v%(version)s.tar.gz']
-patches = [
-    'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch',
-    'Libint-2.6.0_remove-test-eri.patch',
-]
-checksums = [
-    '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa',  # v2.6.0.tar.gz
-    # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch
-    'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab',
-    # Libint-2.6.0_remove-test-eri.patch
-    'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b',
-]
-
-builddependencies = [
-    ('Autotools', '20220317'),
-    ('GMP', '6.2.1'),
-    ('Boost', '1.79.0'),
-    ('Eigen', '3.4.0'),
-    ('Python', '3.10.4'),
-]
-
-# configure options as required by CP2K,
-# see Jenkinsfile in https://github.com/cp2k/libint-cp2k
-local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1)
-local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1)
-
-libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax
-libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am
-libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am
-libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am
-libint_compiler_configopts += '--enable-generic-code --disable-unrolling'
-
-with_fortran = True
-
-moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb
deleted file mode 100644
index 8775e1beada..00000000000
--- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb
+++ /dev/null
@@ -1,60 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'PLUMED'
-version = '2.8.0'
-
-homepage = 'https://www.plumed.org'
-description = """PLUMED is an open source library for free energy calculations in molecular systems which
- works together with some of the most popular molecular dynamics engines. Free energy calculations can be
- performed as a function of many order parameters with a particular  focus on biological problems, using
- state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
- The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
-"""
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-toolchainopts = {'usempi': 'True'}
-
-source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
-sources = [SOURCE_TGZ]
-checksums = ['24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82']
-
-builddependencies = [
-    ('xxd', '8.2.4220'),
-]
-
-dependencies = [
-    ('zlib', '1.2.12'),
-    ('GSL', '2.7'),
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('Boost', '1.79.0'),
-]
-
-preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
-configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
-configopts += '--enable-boost_graph --enable-boost_serialization '
-configopts += '--enable-asmjit '
-prebuildopts = 'source sourceme.sh && '
-
-# make sure that ld.gold linker is used
-# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
-# (problem with intel build but maintain consistency between easyconfigs)
-buildopts = 'LD_RO="ld.gold -r -o"'
-
-# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
-preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
-
-sanity_check_paths = {
-    'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
-    'dirs': [],
-}
-
-sanity_check_commands = ["python -c 'import plumed'"]
-
-modextrapaths = {
-    'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
-    'PLUMED_ROOT': 'lib/plumed',
-    'PYTHONPATH': 'lib/plumed/python',
-}
-
-moduleclass = 'chem'

From 92f4183e5e24c377ef53100b0cbc461bfcc7b4eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 17 Apr 2023 11:09:26 +0200
Subject: [PATCH 349/601] adding easyconfigs: GL2PS-1.4.2-GCCcore-11.3.0.eb,
 GL2PS-1.4.2-GCCcore-12.2.0.eb, freeglut-3.4.0-GCCcore-12.2.0.eb

---
 .../freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb | 39 +++++++++++++++++++
 .../g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb     | 34 ++++++++++++++++
 .../g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb     | 34 ++++++++++++++++
 3 files changed, 107 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..0f9d2c52215
--- /dev/null
+++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'CMakeMake'
+
+name = 'freeglut'
+version = '3.4.0'
+
+homepage = 'http://freeglut.sourceforge.net/'
+description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['3c0bcb915d9b180a97edaebd011b7a1de54583a838644dcd42bb0ea0c6f3eaec']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('X11', '20221110'),
+    ('Mesa', '22.2.4'),
+    ('libGLU', '9.0.2'),
+]
+
+configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT
+configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" '
+configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT
+configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT
+configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" '
+configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT
+configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" '
+
+sanity_check_paths = {
+    'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)],
+    'dirs': ['include/GL'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..46eedfaa2df
--- /dev/null
+++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'GL2PS'
+version = '1.4.2'
+
+homepage = 'https://www.geuz.org/gl2ps/'
+description = """GL2PS: an OpenGL to PostScript printing library"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://geuz.org/gl2ps/src/']
+sources = [SOURCELOWER_TGZ]
+checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('X11', '20220504'),
+    ('Mesa', '22.0.3'),
+    ('libGLU', '9.0.2'),
+    ('freeglut', '3.2.2'),
+    ('libpng', '1.6.37'),
+    ('zlib', '1.2.12'),
+]
+
+sanity_check_paths = {
+    'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..6bd5ffab398
--- /dev/null
+++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'GL2PS'
+version = '1.4.2'
+
+homepage = 'https://www.geuz.org/gl2ps/'
+description = """GL2PS: an OpenGL to PostScript printing library"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://geuz.org/gl2ps/src/']
+sources = [SOURCELOWER_TGZ]
+checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('X11', '20221110'),
+    ('Mesa', '22.2.4'),
+    ('libGLU', '9.0.2'),
+    ('freeglut', '3.4.0'),
+    ('libpng', '1.6.38'),
+    ('zlib', '1.2.12'),
+]
+
+sanity_check_paths = {
+    'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'vis'

From bdef0d696b58bcdefe0dd4669f79f3db75d9f90f Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 17 Apr 2023 15:23:44 +0200
Subject: [PATCH 350/601] adding easyconfigs: BoltzTraP2-22.12.1-foss-2022a.eb,
 pyFFTW-0.13.1-foss-2022a.eb and patches:
 BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch

---
 .../BoltzTraP2-22.12.1-foss-2022a.eb          | 44 ++++++++++++++++
 ...ltzTraP2-22.12.1_use_EB_spglib+eigen.patch | 51 +++++++++++++++++++
 .../p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb      | 24 +++++++++
 3 files changed, 119 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch
 create mode 100755 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb
new file mode 100644
index 00000000000..8f1717a32bb
--- /dev/null
+++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb
@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'BoltzTraP2'
+version = '22.12.1'
+
+homepage = 'https://www.boltztrap.org'
+description = """BoltzTraP2 provides a numerically stable and efficient
+method for obtaining analytic representations of electronic bands based
+on density-functional-theory results for relatively sparse grids. It
+achieves this goal by using smoothed Fourier interpolation."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('pyFFTW', '0.13.1'),
+    ('spglib', '2.0.2'),
+    ('Eigen', '3.4.0'),
+    ('matplotlib', '3.5.2'),
+    ('ASE', '3.22.1'),
+    ('netcdf4-python', '1.6.1'),
+    ('VTK', '9.2.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'modulename': 'BoltzTraP2',
+        'patches': ['BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch'],
+        'checksums': [
+            {'BoltzTraP2-22.12.1.tar.gz': '8338d600c509705e40c834b5431ee8a556d87b06aa1a09853031960a1ff65b3e'},
+            {'BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch':
+             '63791c73ffcb36c0615111377ac5666abfce48872800d3bcc8c93113e37c9030'},
+        ],
+    }),
+]
+
+moduleclass =  'phys'
diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch
new file mode 100644
index 00000000000..ccf7129bb7b
--- /dev/null
+++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch
@@ -0,0 +1,51 @@
+Use spglib and Eigen from EB install
+
+Åke Sandgren, 2023-04-17
+diff -ru BoltzTraP2-22.12.1.orig/setup.py BoltzTraP2-22.12.1/setup.py
+--- BoltzTraP2-22.12.1.orig/setup.py	2022-12-19 19:38:59.000000000 +0100
++++ BoltzTraP2-22.12.1/setup.py	2023-04-17 12:32:46.654682662 +0200
+@@ -187,7 +187,8 @@
+ 
+     def run(self):
+         """Run build_spglib and then delegate on the normal build_ext."""
+-        self.run_command("build_spglib")
++        # Use spglib from EB installation
++        # self.run_command("build_spglib")
+         DefaultBuildExtCommand.run(self)
+ 
+ 
+@@ -213,12 +214,6 @@
+ else:
+     extension = "cpp"
+ 
+-eigen_dir = os.path.abspath(
+-    os.path.join(
+-        os.path.dirname(__file__), "external", "eigen-eigen-3215c06819b9"
+-    )
+-)
+-
+ extensions = [
+     Extension(
+         "BoltzTraP2.sphere.frontend",
+@@ -228,10 +223,10 @@
+         ],
+         language="c++",
+         include_dirs=INCLUDE_DIRS
+-        + [np.get_include(), BuildSPGlibCommand.header_dir, eigen_dir],
++        + [np.get_include()],
+         library_dirs=LIBRARY_DIRS,
+         runtime_library_dirs=LIBRARY_DIRS,
+-        extra_objects=[BuildSPGlibCommand.static_library],
++        libraries = ['symspg'],
+     )
+ ]
+ 
+@@ -282,8 +277,6 @@
+     ext_modules=extensions,
+     cmdclass={
+         "build_ext": BuildExtCommand,
+-        "build_spglib": BuildSPGlibCommand,
+-        "clean_spglib": CleanSPGlibCommand,
+     },
+     install_requires=[
+         "spglib",
diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb
new file mode 100755
index 00000000000..fa32aafe1c2
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'pyFFTW'
+version = '0.13.1'
+
+homepage = 'https://github.com/pyFFTW/pyFFTW'
+description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface
+ for all the supported transforms."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['09155e90a0c6d0c1f2d1f3668180a7de95fb9f83fef5137a112fb05978e87320']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

From bdc3b270faec9d34aa239feb792014061d370197 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 17 Apr 2023 15:27:01 +0200
Subject: [PATCH 351/601] Include Viktors fixes

---
 ...ch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 45 +++++++++++++------
 1 file changed, 31 insertions(+), 14 deletions(-)

diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
index 62ab4bc5ff8..de2c1894efa 100644
--- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -10,48 +10,65 @@ description = """PyTorch with compatible versions of official Torch extensions."
 toolchain = {'name': 'foss', 'version': '2022a'}
 
 builddependencies = [
+    ('CMake', '3.23.1'),
     ('RE2', '2022-06-01'),  # for torchtext
 ]
 
 dependencies = [
     ('CUDA', '11.7.0', '', SYSTEM),
+    ('Python', '3.10.4'),
     ('PyTorch', version, versionsuffix),
     ('Pillow-SIMD', '9.2.0'),  # for torchvision
     ('SentencePiece', '0.1.97'),  # for torchtext
     ('tqdm', '4.64.0'),  # for torchtext
     ('double-conversion', '3.2.0'),  # for torchtext
+    ('utf8proc', '2.7.0'),  # for torchtext
+    ('tensorboard', '2.10.0'),  # for torch-tb-profiler
 ]
 
 use_pip = True
 
 exts_list = [
-    ('torchvision', '0.14.1', {
-        'source_urls': ['https://github.com/pytorch/vision/archive'],
+    ('portalocker', '2.7.0', {
+        'checksums': ['032e81d534a88ec1736d03f780ba073f047a06c478b06e2937486f334e955c51'],
+    }),
+    ('torchdata', '0.4.1', {
+        'preinstallopts': "USE_SYSTEM_LIBS=1 ",
+        'source_urls': ['https://github.com/pytorch/data/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'],
+        'checksums': ['71c0aa3aca3b04a986a2cd4cc2e0be114984ca836dc4def2c700bf1bd1ff087e'],
     }),
-    ('torchtext', '0.14.1', {
-        # Disable bundled libraries to use those from EB: RE2, SentencePiece
-        'preinstallopts': "sed -i '/third_party/d;/BuildExtension/d' setup.py &&",
+    ('torchtext', '0.13.1', {
         'source_urls': ['https://github.com/pytorch/text/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'],
+        'patches': [
+            'torchtext-0.13.1_use-system-libs.patch',
+            'torchtext-0.13.1_deps-fix.patch',
+        ],
+        'checksums': [
+            {'torchtext-0.13.1.tar.gz': '1f7de1fd8c6303ea13ef2aed48a6df67df5f92d1c4a6918253be7decd93753be'},
+            {'torchtext-0.13.1_use-system-libs.patch':
+             'fa899453bd826141ea98f2736a67d255b3a8941c6ca2a236fc352850364efdcc'},
+            {'torchtext-0.13.1_deps-fix.patch': '6e7a9bb854d68eecc70567b92cfbc26f6547aea3f65d4b5cf79cbb19ea43a192'},
+        ],
     }),
-    ('torchaudio', '0.13.1', {
-        'source_urls': ['https://github.com/pytorch/audio/archive'],
+    ('torchvision', '0.13.1', {
+        'source_urls': ['https://github.com/pytorch/vision/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['3a5c108a9ea31d0e6533a2cd6cbaf133efaefe4bdcb4b689183a33b991c95d12'],
+        'checksums': ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'],
     }),
     ('pytorch-ignite', '0.4.11', {
+        'modulename': 'ignite',
         'source_urls': ['https://github.com/pytorch/ignite/archive'],
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'],
     }),
-    ('torchdata', '0.5.1', {
-        'source_urls': ['https://github.com/pytorch/data/archive'],
-        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
-        'checksums': ['69d80bd33ce8f08e7cfeeb71cefddfc29cede25a85881e33dbae47576b96ed29'],
+    ('torch-tb-profiler', '0.4.1', {
+        'modulename': 'torch.profiler',
+        'sources': ['torch_tb_profiler-%(version)s.tar.gz'],
+        'checksums': ['f2c7fb27d420be443ffde50ada655c19f76a245d21e7772de753196fd0967685'],
     }),
+    # torchaudio-0.12.1 needs more work before it can be added
 ]
 
 sanity_pip_check = True

From dfcc41ce59d6c5a87b2adcaf4c7348440b00bc6b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 17 Apr 2023 15:44:53 +0200
Subject: [PATCH 352/601] Fix patch descriptions

---
 ...ch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb |  6 +-
 .../torchtext-0.13.1_cxx_17.patch             | 19 ++++++
 .../torchtext-0.13.1_use-system-libs.patch    | 67 +++++++++++++++++++
 3 files changed, 89 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch
 create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch

diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
index de2c1894efa..17069b4ee78 100644
--- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -43,13 +43,13 @@ exts_list = [
         'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'patches': [
             'torchtext-0.13.1_use-system-libs.patch',
-            'torchtext-0.13.1_deps-fix.patch',
+            'torchtext-0.13.1_cxx_17.patch',
         ],
         'checksums': [
             {'torchtext-0.13.1.tar.gz': '1f7de1fd8c6303ea13ef2aed48a6df67df5f92d1c4a6918253be7decd93753be'},
             {'torchtext-0.13.1_use-system-libs.patch':
-             'fa899453bd826141ea98f2736a67d255b3a8941c6ca2a236fc352850364efdcc'},
-            {'torchtext-0.13.1_deps-fix.patch': '6e7a9bb854d68eecc70567b92cfbc26f6547aea3f65d4b5cf79cbb19ea43a192'},
+             '3e2f170a2870ac274f452b53862f65e5e94f6da1c3af488aeb3001e0500cb0e5'},
+            {'torchtext-0.13.1_cxx_17.patch': 'fd242c139baa27352d1065cece4658a3ede76f46ffec08ac04a554301e547f22'},
         ],
     }),
     ('torchvision', '0.13.1', {
diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch
new file mode 100644
index 00000000000..c980e7c2ebf
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch
@@ -0,0 +1,19 @@
+The error "string_view has not been declared in std" appears when not using C++17
+Split from "deps_fix" patch from torchtext
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1ead15d46..879118c60 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -24,10 +24,10 @@ string(FIND "${CMAKE_CXX_FLAGS}" "-std=c++" env_cxx_standard)
+ if(env_cxx_standard GREATER -1)
+   message(
+       WARNING "C++ standard version definition detected in environment variable."
+-      "PyTorch requires -std=c++14. Please remove -std=c++ settings in your environment.")
++      "PyTorch requires -std=c++17. Please remove -std=c++ settings in your environment.")
+ endif()
+ 
+-set(CMAKE_CXX_STANDARD 14)
++set(CMAKE_CXX_STANDARD 17)
+ set(CMAKE_C_STANDARD 11)
+ 
+ set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch
new file mode 100644
index 00000000000..d0902da8c9e
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch
@@ -0,0 +1,67 @@
+Use external deps for third party libraries
+Split from "deps_fix" patch from torchtext
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1ead15d46..21f85e555 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -63,5 +63,9 @@ endif()
+ # TORCH_CXX_FLAGS contains the same -D_GLIBCXX_USE_CXX11_ABI value as PyTorch
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall ${TORCH_CXX_FLAGS}")
+ 
+-add_subdirectory(third_party)
++find_package(double-conversion)
++find_package(re2)
++find_library(SENTENCEPIECE_LIBRARY sentencepiece PATHS $ENV{EBROOTSENTENCEPIECE}/lib64)
++find_library(SENTENCEPIECE_TRAIN_LIBRARY sentencepiece_train PATHS $ENV{EBROOTSENTENCEPIECE}/lib64)
++find_library(UTF8PROC_LIBRARY utf8proc PATHS $ENV{UTF8PROC}/lib64)
+ add_subdirectory(torchtext/csrc)
+diff --git a/packaging/build_wheel.sh b/packaging/build_wheel.sh
+index 9882cb1b2..43e2a05d8 100755
+--- a/packaging/build_wheel.sh
++++ b/packaging/build_wheel.sh
+@@ -10,7 +10,6 @@ setup_env
+ setup_wheel_python
+ pip_install numpy future cmake>=3.18.0 ninja
+ setup_pip_pytorch_version
+-git submodule update --init --recursive
+ python setup.py clean
+ if [[ "$OSTYPE" == "msys" ]]; then
+     "$script_dir/vc_env_helper.bat" python setup.py bdist_wheel
+diff --git a/setup.py b/setup.py
+index 080415f7e..bd84405be 100644
+--- a/setup.py
++++ b/setup.py
+@@ -68,7 +68,6 @@ class clean(distutils.command.clean.clean):
+         # Remove build directory
+         build_dirs = [
+             ROOT_DIR / "build",
+-            ROOT_DIR / "third_party" / "build",
+         ]
+         for path in build_dirs:
+             if path.exists():
+diff --git a/torchtext/csrc/CMakeLists.txt b/torchtext/csrc/CMakeLists.txt
+index 037f814dc..658b90342 100644
+--- a/torchtext/csrc/CMakeLists.txt
++++ b/torchtext/csrc/CMakeLists.txt
+@@ -24,10 +24,6 @@ set(
+ set(
+   LIBTORCHTEXT_INCLUDE_DIRS
+   ${PROJECT_SOURCE_DIR}
+-  ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src
+-  $<TARGET_PROPERTY:re2,INCLUDE_DIRECTORIES>
+-  $<TARGET_PROPERTY:double-conversion,INCLUDE_DIRECTORIES>
+-  $<TARGET_PROPERTY:utf8proc,INCLUDE_DIRECTORIES>
+   ${TORCH_INSTALL_PREFIX}/include
+   ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include
+   )
+@@ -123,10 +119,6 @@ if (BUILD_TORCHTEXT_PYTHON_EXTENSION)
+   set(
+     EXTENSION_INCLUDE_DIRS
+     ${PROJECT_SOURCE_DIR}
+-    ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src
+-    $<TARGET_PROPERTY:re2,INCLUDE_DIRECTORIES>
+-    $<TARGET_PROPERTY:double-conversion,INCLUDE_DIRECTORIES>
+-    $<TARGET_PROPERTY:utf8proc,INCLUDE_DIRECTORIES>
+     ${TORCH_INSTALL_PREFIX}/include
+     ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include
+     )

From f7469fa2e8743cdbaebf99be38bd5d30f2ba4f02 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 17 Apr 2023 15:49:16 +0200
Subject: [PATCH 353/601] adding easyconfigs: ROOT-6.26.10-foss-2022b.eb

---
 .../r/ROOT/ROOT-6.26.10-foss-2022b.eb         | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb

diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb
new file mode 100644
index 00000000000..4acf0146bc4
--- /dev/null
+++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb
@@ -0,0 +1,55 @@
+name = 'ROOT'
+version = '6.26.10'
+
+homepage = 'https://root.cern.ch/drupal/'
+description = """The ROOT system provides a set of OO frameworks with all the functionality
+    needed to handle and analyze large amounts of data in a very efficient way."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://root.cern.ch/download/']
+sources = ['%(namelower)s_v%(version)s.source.tar.gz']
+checksums = ['8e56bec397104017aa54f9eb554de7a1a134474fe0b3bb0f43a70fc4fabd625f']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('pkgconf', '1.9.3'),
+]
+
+dependencies = [
+    ('GSL', '2.7'),
+    ('libxml2', '2.10.3'),
+    ('PCRE', '8.45'),
+    ('CFITSIO', '4.2.0'),
+    ('freetype', '2.12.1'),
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('zlib', '1.2.12'),
+    ('X11', '20221110'),
+    ('Mesa', '22.2.4'),
+    ('libGLU', '9.0.2'),
+    ('GL2PS', '1.4.2'),
+    ('FFTW', '3.3.10'),
+    ('SQLite', '3.39.4'),
+    ('XZ', '5.2.7'),
+    ('libpng', '1.6.38'),
+]
+
+# NOTE: Ensure that each configopts string begins with a blank
+# disable some components
+configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF"
+
+# make sure some components are enabled
+configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON"
+configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON "
+
+# Add component-specific settings based on dependencies
+configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND'
+
+# Set C++ standard to C++17 for better stability
+configopts += ' -DCMAKE_CXX_STANDARD=17'
+
+configopts += " -Dgallium-drivers=swrast"
+
+moduleclass = 'data'

From 145138485cedb77a8cbee01bdc05274a27790174 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 17 Apr 2023 16:00:04 +0200
Subject: [PATCH 354/601] Drop CMake since it is not really needed and fix
 extra space.

---
 .../b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb           | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb
index 8f1717a32bb..663a6d225c6 100644
--- a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb
@@ -11,10 +11,6 @@ achieves this goal by using smoothed Fourier interpolation."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
-builddependencies = [
-    ('CMake', '3.23.1'),
-]
-
 dependencies = [
     ('Python', '3.10.4'),
     ('pyFFTW', '0.13.1'),
@@ -41,4 +37,4 @@ exts_list = [
     }),
 ]
 
-moduleclass =  'phys'
+moduleclass = 'phys'

From 58d65f2cc237434c3f789c1bfa6e400ba5b27cf2 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Mon, 17 Apr 2023 15:15:19 +0100
Subject: [PATCH 355/601] exclude test_optim

---
 .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb       | 3 +++
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 3 +++
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb       | 5 ++++-
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 3 +++
 .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb       | 3 +++
 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 3 +++
 6 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
index 9778d40af76..dba21cb3e1e 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
@@ -122,6 +122,9 @@ excluded_tests = {
     '': [
         # This test seems to take too long on NVIDIA Ampere at least.
         'distributed/test_distributed_spawn',
+        # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
+        # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
+        'test_optim',
     ]
 }
 
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
index 4417c0cacee..5a1a052ef23 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
@@ -111,6 +111,9 @@ excluded_tests = {
     '': [
         # This test seems to take too long on NVIDIA Ampere at least.
         'distributed/test_distributed_spawn',
+        # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
+        # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
+        'test_optim',
     ]
 }
 
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
index 7d0cc431687..4bbdb824152 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -146,7 +146,10 @@ excluded_tests = {
         'distributed/fsdp/test_fsdp_core',
         # failing on broadwell
         # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
-        'test_native_mha'
+        'test_native_mha',
+        # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
+        # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
+        'test_optim',
     ]
 }
 
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
index 7c58b58e5fd..9f564b7abe1 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
@@ -128,6 +128,9 @@ excluded_tests = {
         # flaky test which fails on some systems,
         # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
         'distributed/elastic/multiprocessing/api_test',
+        # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
+        # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
+        'test_optim',
     ]
 }
 
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
index 528fb671557..e10e5221763 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -140,6 +140,9 @@ excluded_tests = {
         # Those 2 abort on some machines. Skip for now
         'distributed/fsdp/test_fsdp_input',
         'distributed/fsdp/test_fsdp_mixed_precision',
+        # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
+        # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
+        'test_optim',
     ]
 }
 
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
index c31da630572..6768a396213 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
@@ -123,6 +123,9 @@ excluded_tests = {
         'distributed/test_distributed_spawn',
         # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375
         'distributions/test_constraints',
+        # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
+        # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
+        'test_optim',
     ]
 }
 

From 40c0644024f645fcf2848def93d18cddddd99a7c Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Mon, 17 Apr 2023 15:26:50 +0100
Subject: [PATCH 356/601] add test excludes documented in 17615 to all 1.12.1
 easyconfigs

---
 .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb   | 9 +++++++++
 .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb   | 9 +++++++++
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb   | 3 +++
 .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb   | 3 +++
 .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb   | 9 +++++++++
 .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb   | 9 +++++++++
 6 files changed, 42 insertions(+)

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
index dba21cb3e1e..df2f07b6db3 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
@@ -122,6 +122,15 @@ excluded_tests = {
     '': [
         # This test seems to take too long on NVIDIA Ampere at least.
         'distributed/test_distributed_spawn',
+        # Produces a single test failure on some systems
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/fsdp/test_fsdp_core',
+        # failing on broadwell
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'test_native_mha',
+        # flaky test which fails on some systems,
+        # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/elastic/multiprocessing/api_test',
         # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
         # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
         'test_optim',
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
index 5a1a052ef23..550c24d748b 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
@@ -111,6 +111,15 @@ excluded_tests = {
     '': [
         # This test seems to take too long on NVIDIA Ampere at least.
         'distributed/test_distributed_spawn',
+        # Produces a single test failure on some systems
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/fsdp/test_fsdp_core',
+        # failing on broadwell
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'test_native_mha',
+        # flaky test which fails on some systems,
+        # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/elastic/multiprocessing/api_test',
         # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
         # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
         'test_optim',
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
index 4bbdb824152..3ce09263594 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -147,6 +147,9 @@ excluded_tests = {
         # failing on broadwell
         # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
         'test_native_mha',
+        # flaky test which fails on some systems,
+        # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/elastic/multiprocessing/api_test',
         # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
         # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
         'test_optim',
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
index 9f564b7abe1..b4ca5e1483a 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
@@ -122,6 +122,9 @@ excluded_tests = {
     '': [
         # This test seems to take too long on NVIDIA Ampere at least.
         'distributed/test_distributed_spawn',
+        # Produces a single test failure on some systems
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/fsdp/test_fsdp_core',
         # failing on broadwell
         # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
         'test_native_mha',
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
index e10e5221763..8cc442f469d 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -140,6 +140,15 @@ excluded_tests = {
         # Those 2 abort on some machines. Skip for now
         'distributed/fsdp/test_fsdp_input',
         'distributed/fsdp/test_fsdp_mixed_precision',
+        # Produces a single test failure on some systems
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/fsdp/test_fsdp_core',
+        # failing on broadwell
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'test_native_mha',
+        # flaky test which fails on some systems,
+        # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/elastic/multiprocessing/api_test',
         # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
         # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
         'test_optim',
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
index 6768a396213..3f02df492ba 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
@@ -123,6 +123,15 @@ excluded_tests = {
         'distributed/test_distributed_spawn',
         # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375
         'distributions/test_constraints',
+        # Produces a single test failure on some systems
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/fsdp/test_fsdp_core',
+        # failing on broadwell
+        # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'test_native_mha',
+        # flaky test which fails on some systems,
+        # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615
+        'distributed/elastic/multiprocessing/api_test',
         # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079
         # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414
         'test_optim',

From ca7f8e07bd86b8bcb279134f15857ee83b9fcadc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 17 Apr 2023 17:50:00 +0200
Subject: [PATCH 357/601] adding easyconfigs: PYTHIA-8.309-foss-2022b.eb

---
 .../p/PYTHIA/PYTHIA-8.309-foss-2022b.eb       | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb
new file mode 100644
index 00000000000..e664b716b74
--- /dev/null
+++ b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb
@@ -0,0 +1,42 @@
+easyblock = 'ConfigureMake'
+
+name = 'PYTHIA'
+version = '8.309'
+
+homepage = 'https://www.pythia.org'
+description = """PYTHIA is a program for the generation of high-energy physics collision events, i.e. for the
+description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory
+and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and
+final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original
+research, but also borrows many formulae and other knowledge from the literature. As such it is categorized as a
+general purpose Monte Carlo event generator."""
+
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.pythia.org/download/pythia83/']
+sources = ['pythia%(version_major)s%(version_minor)s.tgz']
+checksums = ['5bdafd9f2c4a1c47fd8a4e82fb9f0d8fcfba4de1003b8e14be4e0347436d6c33']
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('Python', '3.10.8'),
+    ('ROOT', '6.26.10'),
+    ('HDF5', '1.14.0'),
+]
+
+configopts = '--cxx="$CXX" --cxx-common="$CXXFLAGS" '
+configopts += '--with-openmp --with-mpich --with-gzip --with-root --with-hdf5 '
+configopts += '--with-python --with-python-include=$EBROOTPYTHON/include/python*/ '
+
+sanity_check_paths = {
+    'files': ['bin/pythia%(version_major)s-config', 'lib/libpythia%(version_major)s.a',
+              'lib/libpythia%%(version_major)s.%s' % SHLIB_EXT, 'lib/pythia8.%s' % SHLIB_EXT],
+    'dirs': ['include/Pythia%(version_major)s', 'include/Pythia%(version_major)sPlugins', 'share'],
+}
+sanity_check_commands = ["python -c 'import pythia%(version_major)s'"]
+
+modextrapaths = {'PYTHONPATH': 'lib'}
+
+moduleclass = 'phys'

From 2cdfef6c096493e071f7c00ecb2ce98cbd8d3210 Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 18 Apr 2023 00:52:56 +0200
Subject: [PATCH 358/601] Add espresso 4.2.1

---
 ... ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} |  0
 .../ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb  | 53 +++++++++++++++++++
 2 files changed, 53 insertions(+)
 rename easybuild/easyconfigs/e/ESPResSo/{ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb => ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} (100%)
 create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb
similarity index 100%
rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb
rename to easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb
diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
new file mode 100644
index 00000000000..3924a2baf37
--- /dev/null
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
@@ -0,0 +1,53 @@
+easyblock = 'CMakeMake'
+
+name = 'ESPResSo'
+version = '4.2.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://espressomd.org/wordpress'
+description = """A software package for performing and analyzing scientific Molecular Dynamics simulations."""
+
+source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255']
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+builddependencies = [('CMake', '3.20.1')]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('CUDA', '11.3.1', '', SYSTEM),
+    ('SciPy-bundle', '2021.05'),
+    ('Boost.MPI', '1.76.0'),
+    ('HDF5', '1.10.7'),
+    ('Mesa', '21.1.1'),
+    ('GSL', '2.7'),
+    ('IPython', '7.25.0'),
+    ('Pint', '0.20.1'),
+]
+
+configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON'
+
+runtest = 'check_unit_tests && make check_python'
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+_binaries = ['ipypresso',  'pypresso']
+_libs = [
+    'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes',
+    '_init', 'analyze', 'code_info', 'cuda_init', 'electrokinetics', 'galilei',
+    'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler',
+    'script_interface', 'system', 'thermostat', 'utils', 'version',
+]
+
+_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _binaries] +
+             [_lib_path + f'/%s.{SHLIB_EXT}' % x for x in _libs],
+    'dirs': ['bin', 'lib']
+}
+
+moduleclass = 'chem'

From 0b7899aa0af4f289934fb7cebffa8dcaba3e178a Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 18 Apr 2023 00:54:20 +0200
Subject: [PATCH 359/601] Remove v4.2.0

---
 .../ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb  | 54 -------------------
 1 file changed, 54 deletions(-)
 delete mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb
deleted file mode 100644
index 51fa7dc8424..00000000000
--- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb
+++ /dev/null
@@ -1,54 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'ESPResSo'
-version = '4.2.0'
-versionsuffix = '-CUDA-%(cudaver)s'
-
-homepage = 'https://espressomd.org/wordpress'
-description = """A software package for performing and analyzing scientific Molecular Dynamics simulations."""
-
-source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/']
-sources = ['%(version)s.tar.gz']
-checksums = ['e6e17fafa9ba80b46f542dc86e07677a8d641cfd0102ebc4db2f7ee47d5fb6f1']
-
-toolchain = {'name': 'foss', 'version': '2021a'}
-toolchainopts = {'usempi': True, 'pic': True}
-
-builddependencies = [('CMake', '3.20.1')]
-
-dependencies = [
-    ('Python', '3.9.5'),
-    ('CUDA', '11.3.1', '', SYSTEM),
-    ('SciPy-bundle', '2021.05'),
-    ('Boost.MPI', '1.76.0'),
-    ('Cython', '0.29.34'),
-    ('HDF5', '1.10.7'),
-    ('Mesa', '21.1.1'),
-    ('GSL', '2.7'),
-    ('IPython', '7.25.0'),
-    ('Pint', '0.20.1'),
-]
-
-configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON'
-
-separate_build_dir = True
-
-modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
-
-_binaries = ['ipypresso',  'pypresso']
-_libs = [
-    'Espresso_config.so', 'Espresso_core.so', 'Espresso_script_interface.so', 'Espresso_shapes.so',
-    '_init.so', 'analyze.so', 'code_info.so', 'cuda_init.so', 'electrokinetics.so', 'galilei.so',
-    'integrate.so', 'interactions.so', 'lb.so', 'particle_data.so', 'polymer.so', 'profiler.so',
-    'script_interface.so', 'system.so', 'thermostat.so', 'utils.so', 'version.so',
-]
-
-_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'
-
-sanity_check_paths = {
-    'files': ['bin/%s' % x for x in _binaries] +
-             [_lib_path + '/%s' % x for x in _libs],
-    'dirs': ['bin', 'lib']
-}
-
-moduleclass = 'chem'

From 2e438593742a1a64f5121e59d9da1a02b02e505f Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 18 Apr 2023 00:55:50 +0200
Subject: [PATCH 360/601] Remove Cython

---
 .../c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb | 38 -------------------
 1 file changed, 38 deletions(-)
 delete mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb
deleted file mode 100644
index faff04ca575..00000000000
--- a/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb
+++ /dev/null
@@ -1,38 +0,0 @@
-easyblock = 'PythonPackage'
-
-name = 'Cython'
-version = '0.29.34'
-
-homepage = 'https://cython.org/'
-description = """
-Cython is an optimising static compiler for both the Python programming
-language and the extended Cython programming language (based on Pyrex).
-"""
-docurls = [
-    'https://cython.org/#documentation',
-    'https://github.com/cython/cython',
-]
-
-toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
-
-sources = [SOURCE_TAR_GZ]
-checksums = ['1909688f5d7b521a60c396d20bba9e47a1b2d2784bfb085401e1e1e7d29a29a8']
-
-builddependencies = [('binutils', '2.36.1')]
-
-dependencies = [('Python', '3.9.5')]
-
-download_dep_fail = True
-use_pip = True
-sanity_pip_check = True
-
-sanity_check_paths = {
-    'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
-    'dirs': ['lib/python%(pyshortver)s/site-packages'],
-}
-
-sanity_check_commands = [
-    'cython --version',
-]
-
-moduleclass = 'lang'

From fef63e850bb980fd82af9d3e39368d6b8f8aabd5 Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 18 Apr 2023 00:59:13 +0200
Subject: [PATCH 361/601] Add sanity check cmds

---
 .../e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb         | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
index 3924a2baf37..8bf837144e0 100644
--- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
@@ -50,4 +50,6 @@ sanity_check_paths = {
     'dirs': ['bin', 'lib']
 }
 
+sanity_check_commands = ['pypresso -h', 'ipypresso -h']
+
 moduleclass = 'chem'

From 1f5ab2097618bfe8abf21cc25db4e014d513e834 Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Tue, 18 Apr 2023 09:05:45 +0200
Subject: [PATCH 362/601] adding easyconfigs: make-4.4.1-GCCcore-12.2.0.eb

---
 .../m/make/make-4.4.1-GCCcore-12.2.0.eb       | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..a4107e59ee5
--- /dev/null
+++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'make'
+version = '4.4.1'
+
+homepage = 'https://www.gnu.org/software/make/make.html'
+description = "GNU version of make utility"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3']
+
+builddependencies = [('binutils', '2.39')]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"]
+
+sanity_check_paths = {
+    'files': ['bin/gmake', 'bin/make'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "gmake --help",
+    "make --help",
+]
+
+moduleclass = 'devel'

From d998e393444848e1bd7aa76836b73eb460d04aea Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 18 Apr 2023 11:01:57 +0200
Subject: [PATCH 363/601] Adapt for python-2

---
 .../e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
index 8bf837144e0..a8901cbb3d1 100644
--- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb
@@ -46,7 +46,7 @@ _lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd'
 
 sanity_check_paths = {
     'files': ['bin/%s' % x for x in _binaries] +
-             [_lib_path + f'/%s.{SHLIB_EXT}' % x for x in _libs],
+             [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs],
     'dirs': ['bin', 'lib']
 }
 

From b6a44a2cc67045a5289a018cebe1399fe0220e17 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Tue, 18 Apr 2023 10:33:22 +0100
Subject: [PATCH 364/601] adding easyconfigs: GenMap-1.3.0-GCCcore-11.2.0.eb

---
 .../g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb   | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100755 easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb

diff --git a/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb
new file mode 100755
index 00000000000..2a1f332ae41
--- /dev/null
+++ b/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'GenMap'
+version = '1.3.0'
+
+homepage = 'https://github.com/cpockrandt/genmap'
+
+description = """GenMap - Fast and Exact Computation of Genome Mappability"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.2.0'}
+
+source_urls = ['https://github.com/cpockrandt/genmap/archive/']
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+checksums = ['d237b284bb26d000039078e7be81bbebae21ee65d614ce89bd47a45f99fafb64']
+
+builddependencies = [
+    ('binutils', '2.37'),
+    ('CMake', '3.21.1'),
+    ('Python', '3.9.6'),
+]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.11'),
+    ('SeqAn', '2.4.0'),
+]
+
+configopts = "-DSeqAn_DIR=$EBROOTSEQAN/util/cmake"
+
+sanity_check_paths = {
+    'files': ["bin/genmap"],
+    'dirs': [],
+}
+
+sanity_check_commands = ["genmap %s --help" % x for x in ["", "index", "map"]]
+
+moduleclass = 'bio'

From 558c33249b51a6a925563f630ac36c441235b21f Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 18 Apr 2023 12:29:21 +0100
Subject: [PATCH 365/601] adding easyconfigs: pyslim-1.0.1-foss-2022a.eb

---
 .../p/pyslim/pyslim-1.0.1-foss-2022a.eb       | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb
new file mode 100644
index 00000000000..da7c91bba12
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonBundle'
+
+name = 'pyslim'
+version = '1.0.1'
+
+homepage = 'https://tskit.dev/pyslim/docs/stable/introduction.html'
+description = """A Python API for reading and modifying tskit tree
+sequence files produced by SLiM, or modifying files produced by other
+programs (e.g., msprime, fwdpy11, and tsinfer) for use in SLiM."""
+
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),  # for numpy
+    ('msprime', '1.2.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['d65923658df9303962997f8911449245d33cf7f56aada8df4573ad301a9934c6'],
+    }),
+]
+
+moduleclass = 'bio'

From de2d32348deff7fda8fd2ed7326bb1b5e3cef6df Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 18 Apr 2023 12:30:56 +0100
Subject: [PATCH 366/601] adding easyconfigs: msprime-1.2.0-foss-2022a.eb

---
 .../m/msprime/msprime-1.2.0-foss-2022a.eb     | 58 +++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb
new file mode 100644
index 00000000000..b5ea22facf2
--- /dev/null
+++ b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb
@@ -0,0 +1,58 @@
+easyblock = 'PythonBundle'
+
+name = 'msprime'
+version = '1.2.0'
+
+homepage = 'https://msprime.readthedocs.io'
+description = "msprime is a coalescent simulator and library for processing tree-based genetic data."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),  # for numpy
+    ('GSL', '2.7'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('svgwrite', '1.4.3', {
+        'source_tmpl': '%(name)s-%(version)s.zip',
+        'checksums': ['a8fbdfd4443302a6619a7f76bc937fc683daf2628d9b737c891ec08b8ce524c3'],
+    }),
+    ('tskit', '0.5.4', {
+        'checksums': ['be1a6381c72a95f0011bea26ca317e1b4503b8d2dcd87096c68aa16c8946c6fe'],
+    }),
+    ('ruamel.yaml.clib', '0.2.7', {
+        'modulename': False,
+        'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'],
+    }),
+    ('ruamel.yaml', '0.17.21', {
+        'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'],
+    }),
+    ('demes', '0.2.2', {
+        'checksums': ['8eebe4b236b2d19e057228892f5b5f53f3e0d127ca9128efead1728a65115dac'],
+    }),
+    ('newick', '1.9.0', {
+        'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'],
+    }),
+    (name, version, {
+        'checksums': ['60025ad9fd30d827a72ae6e760b6cff07a1d0e169b2c1da1024cb0fc23e4a7aa'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/msp', 'bin/mspms', 'bin/tskit', 'bin/demes'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    'demes --help',
+    'tskit --help',
+    'msp --help',
+    'mspms --help',
+]
+
+moduleclass = 'bio'

From 2597a1f4a3833e1050c63049a38ed8bd279a922f Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 18 Apr 2023 12:33:01 +0100
Subject: [PATCH 367/601] adding easyconfigs: SLiM-4.0.1-GCC-11.3.0.eb and
 patches: SLiM-4.0.1_use_external_zlib_gsl.patch

---
 .../s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb           |  48 ++++++
 .../SLiM-4.0.1_use_external_zlib_gsl.patch    | 161 ++++++++++++++++++
 2 files changed, 209 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch

diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb
new file mode 100644
index 00000000000..4d9a4c39ed5
--- /dev/null
+++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb
@@ -0,0 +1,48 @@
+easyblock = 'CMakeMake'
+
+name = 'SLiM'
+version = '4.0.1'
+
+homepage = 'https://messerlab.org/slim'
+description = """SLiM is an evolutionary simulation framework that combines a powerful engine for population
+ genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/MesserLab/%(name)s/archive']
+sources = ['v%(version)s.tar.gz']
+patches = [
+    '%(name)s-%(version)s_use_external_zlib_gsl.patch',
+]
+checksums = [
+    {'v4.0.1.tar.gz': 'a44564023db372cd438b4e6c729a4ba59200d1217a63b3694ca7903436886cc2'},
+    {'SLiM-4.0.1_use_external_zlib_gsl.patch': '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('GSL', '2.7'),
+    ('Mesa', '22.0.3'),
+    ('libglvnd', '1.4.0'),
+    ('Qt5', '5.15.5'),
+]
+
+configopts = '-DBUILD_SLIMGUI=ON '
+
+sanity_check_paths = {
+    'files': ['bin/eidos', 'bin/slim'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "eidos -usage",
+    "eidos -testEidos",
+    "slim -usage",
+    "slim -testSLiM",
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch
new file mode 100644
index 00000000000..894f69dd4f3
--- /dev/null
+++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch
@@ -0,0 +1,161 @@
+commit 2ba4892b9327e5d21fdd712e178447d2ecd3665a
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Wed Aug 24 08:15:39 2022 +0200
+
+    Use external Zlib and GSL instead of internal ones.
+    And use correctly names zlib functions.
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 487c7bcd..0aae03ea 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -157,18 +157,20 @@ endif()
+ #endif()
+ 
+ # GSL 
+-set(TARGET_NAME gsl)
+-file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c)
+-set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg)
+-add_library(${TARGET_NAME} STATIC ${GSL_SOURCES})
+-target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES})
++# Use external GSL instead
++#set(TARGET_NAME gsl)
++#file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c)
++#set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg)
++#add_library(${TARGET_NAME} STATIC ${GSL_SOURCES})
++#target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES})
+ 
+ # ZLIB
+-set(TARGET_NAME eidos_zlib)
+-file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c)
+-set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib)
+-add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES})
+-target_include_directories(${TARGET_NAME} PUBLIC)
++# Use external Zlib instead
++#set(TARGET_NAME eidos_zlib)
++#file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c)
++#set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib)
++#add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES})
++#target_include_directories(${TARGET_NAME} PUBLIC)
+ 
+ # KASTORE
+ set(TARGET_NAME kastore)
+@@ -198,7 +200,7 @@ list(APPEND SLIM_SOURCES "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" ${PROJECT_SOU
+ 
+ add_executable(${TARGET_NAME} ${SLIM_SOURCES})
+ target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/eidos")
+-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables)
++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables)
+ if(WIN32)
+     set_source_files_properties(${SLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
+     set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
+@@ -211,7 +213,7 @@ set(TARGET_NAME eidos)
+ file(GLOB_RECURSE EIDOS_SOURCES  ${PROJECT_SOURCE_DIR}/eidos/*.cpp  ${PROJECT_SOURCE_DIR}/eidostool/*.cpp)
+ add_executable(${TARGET_NAME} ${EIDOS_SOURCES})
+ target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/eidos")
+-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables)
++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables)
+ if(WIN32)
+     set_source_files_properties(${EIDOS_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
+     set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
+@@ -244,15 +246,15 @@ set_target_properties( ${TARGET_NAME} PROPERTIES LINKER_LANGUAGE CXX)
+ target_compile_definitions( ${TARGET_NAME} PRIVATE EIDOSGUI=1 SLIMGUI=1)
+ target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore")
+ if(APPLE)
+-	target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib /usr/lib/libobjc.A.dylib )
++	target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z /usr/lib/libobjc.A.dylib )
+ else()
+     if(WIN32)
+         set_source_files_properties(${QTSLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
+         set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos SLiMgui PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
+         target_include_directories(${TARGET_NAME} BEFORE PUBLIC ${GNU_DIR})
+-        target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib gnu )
++        target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z gnu )
+     else()
+-	    target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib )
++	    target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z )
+     endif()
+ endif()
+ install(TARGETS ${TARGET_NAME} DESTINATION bin)
+diff --git a/eidos/eidos_functions.cpp b/eidos/eidos_functions.cpp
+index 4f52c763..ac9de199 100644
+--- a/eidos/eidos_functions.cpp
++++ b/eidos/eidos_functions.cpp
+@@ -55,11 +55,11 @@
+ 
+ #include "string.h"
+ 
+-#include "gsl_linalg.h"
+-#include "gsl_errno.h"
+-#include "gsl_cdf.h"
++#include <gsl/gsl_linalg.h>
++#include <gsl/gsl_errno.h>
++#include <gsl/gsl_cdf.h>
+ 
+-#include "../eidos_zlib/zlib.h"
++#include <zlib.h>
+ 
+ #include "eidos_globals.h"
+ #if EIDOS_ROBIN_HOOD_HASHING
+@@ -11475,7 +11475,7 @@ EidosValue_SP Eidos_ExecuteFunction_writeTempFile(const std::vector<EidosValue_S
+ 	if (do_compress)
+ 	{
+ 		// compression using zlib; very different from the no-compression case, unfortunately, because here we use C-based APIs
+-		gzFile gzf = z_gzdopen(fd, "wb");
++		gzFile gzf = gzdopen(fd, "wb");
+ 		
+ 		if (!gzf)
+ 		{
+diff --git a/eidos/eidos_globals.cpp b/eidos/eidos_globals.cpp
+index dc801c2f..95984159 100644
+--- a/eidos/eidos_globals.cpp
++++ b/eidos/eidos_globals.cpp
+@@ -65,13 +65,13 @@
+ #endif
+ 
+ // for Eidos_WelchTTest()
+-#include "gsl_cdf.h"
++#include <gsl/gsl_cdf.h>
+ 
+ // for Eidos_calc_sha_256()
+ #include <stdint.h>
+ 
+ // for _Eidos_FlushZipBuffer()
+-#include "../eidos_zlib/zlib.h"
++#include <zlib.h>
+ 
+ // for Eidos_ColorPaletteLookup()
+ #include "eidos_tinycolormap.h"
+@@ -1570,7 +1570,7 @@ bool _Eidos_FlushZipBuffer(const std::string &file_path, const std::string &outs
+ {
+ 	//std::cout << "_Eidos_FlushZipBuffer() called for " << file_path << std::endl;
+ 	
+-	gzFile gzf = z_gzopen(file_path.c_str(), "ab");
++	gzFile gzf = gzopen(file_path.c_str(), "ab");
+ 	
+ 	if (!gzf)
+ 		return false;
+@@ -1678,7 +1678,7 @@ void Eidos_WriteToFile(const std::string &p_file_path, std::vector<const std::st
+ 		{
+ 			// this code can handle both the append and the non-append case, but the append case may generate very low-quality
+ 			// compression (potentially even worse than the uncompressed data) due to having an excess of gzip headers
+-			gzFile gzf = z_gzopen(p_file_path.c_str(), p_append ? "ab" : "wb");
++			gzFile gzf = gzopen(p_file_path.c_str(), p_append ? "ab" : "wb");
+ 			
+ 			if (!gzf)
+ 				EIDOS_TERMINATION << "#ERROR (Eidos_WriteToFile): could not write to file at path " << p_file_path << "." << EidosTerminate(nullptr);
+diff --git a/eidos/eidos_rng.h b/eidos/eidos_rng.h
+index 313f75d7..7ab9db4d 100644
+--- a/eidos/eidos_rng.h
++++ b/eidos/eidos_rng.h
+@@ -29,8 +29,8 @@
+ 
+ // We have our own private copy of (parts of) the GSL library, so that we don't have link dependencies.
+ // See the _README file in the gsl directory for information on the local copy of the GSL included in this project.
+-#include "gsl_rng.h"
+-#include "gsl_randist.h"
++#include <gsl/gsl_rng.h>
++#include <gsl/gsl_randist.h>
+ 
+ #include <stdint.h>
+ #include <cmath>

From 1f2330e2fb7bc7a4e7c79c9f41f4feff70ecb333 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Tue, 18 Apr 2023 13:44:47 +0200
Subject: [PATCH 368/601] adding easyconfigs: Check-0.15.2-GCCcore-11.3.0.eb

---
 .../c/Check/Check-0.15.2-GCCcore-11.3.0.eb    | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..f1ca4ac1035
--- /dev/null
+++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'Check'
+version = '0.15.2'
+
+homepage = 'https://libcheck.github.io/check/'
+description = """
+Check is a unit testing framework for C. It features a simple interface for
+defining unit tests, putting little in the way of the developer. Tests are
+run in a separate address space, so both assertion failures and code errors
+that cause segmentation faults or other signals can be caught. Test results
+are reportable in the following: Subunit, TAP, XML, and a generic logging
+format."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'libcheck'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('Autotools', '20220317'),
+    ('pkgconf', '1.8.0'),
+]
+
+preconfigopts = "autoreconf -f -i && "
+configopts = "--disable-build-docs"
+
+sanity_check_paths = {
+    'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share']
+}
+
+moduleclass = 'lib'

From 4512e49ababe85f69dd7c104a91b2a83309c4607 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 18 Apr 2023 14:52:48 +0200
Subject: [PATCH 369/601] adding easyconfigs:
 ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb, ColabFold-1.5.2-foss-2022a.eb,
 AlphaFold-2.3.4-foss-2022a-ColabFold.eb,
 AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb and patches:
 AlphaFold-ColabFold-2.3.4_data-dep-paths.patch,
 AlphaFold-ColabFold-2.3.4_fix-scp-path.patch

---
 ...-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb | 178 ++++++++++++++++++
 .../AlphaFold-2.3.4-foss-2022a-ColabFold.eb   | 167 ++++++++++++++++
 ...aFold-ColabFold-2.3.4_data-dep-paths.patch | 134 +++++++++++++
 ...phaFold-ColabFold-2.3.4_fix-scp-path.patch |  14 ++
 .../ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb |  58 ++++++
 .../c/ColabFold/ColabFold-1.5.2-foss-2022a.eb |  56 ++++++
 6 files changed, 607 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch
 create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch
 create mode 100644 easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb
 create mode 100644 easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb
new file mode 100644
index 00000000000..51dbe4220f7
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb
@@ -0,0 +1,178 @@
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold'
+version = '2.3.4'
+_colab_suffix = '-ColabFold'
+_cuda_suffix = '-CUDA-%(cudaver)s'
+versionsuffix = _cuda_suffix + _colab_suffix
+_commit = '41807ea2c75706cf03f790f06ca191dc04331e41'
+
+homepage = 'https://github.com/sokrypton/alphafold'
+description = """
+AlphaFold can predict protein structures with atomic accuracy even where no
+similar structure is known.
+This package of AlphaFold contains patches for ColabFold."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    # required for installing dm-tree
+    ('Bazel', '5.1.1'),
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('TensorFlow', '2.11.0', _cuda_suffix),
+    ('Biopython', '1.79'),
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.3.2'),
+    ('Kalign', '3.3.5'),
+    ('jax', '0.3.25', _cuda_suffix),  # also provides absl-py
+    ('UCX-CUDA', '1.12.1', _cuda_suffix),
+    ('cuDNN', '8.4.1.50', _cuda_suffix, SYSTEM),
+    ('NCCL', '2.12.12', _cuda_suffix),
+    ('OpenMM', '8.0.0', _cuda_suffix),
+]
+
+# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
+# see docker/Dockerfile in AlphaFold repository
+local_scp_commit = '7102c6'
+
+components = [
+    (name, version, {
+        'easyblock': 'PythonPackage',
+        'source_urls': [
+            'https://github.com/sokrypton/alphafold/archive/',
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [
+            {
+                'download_filename': '%s.tar.gz' % _commit,
+                'filename': '%s-%s.tar.gz' % (name.lower() + _colab_suffix.lower(), version)
+            },
+            {
+                'download_filename': 'stereo_chemical_props.txt',
+                'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+                'extract_cmd': "cp %s .",
+            },
+        ],
+        'patches': [
+            'AlphaFold-ColabFold-2.3.4_data-dep-paths.patch',
+            'AlphaFold-2.0.0_n-cpu.patch',
+            'AlphaFold-ColabFold-2.3.4_fix-scp-path.patch',
+            'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+            'AlphaFold-2.3.1_use_openmm_7.7.0.patch',
+        ],
+        'checksums': [
+            'be6778333fc110b8662b0e262798d6fc1663a14d9341469c6558b2d7771b8024',  # alphafold-colabfold-2.3.4.tar.gz
+            '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
+            # AlphaFold-ColabFold-2.3.4_data-dep-paths.patch
+            '3826e357c35a58b2c8c0fab41ac8ae1b4d4c135162fe47ded577a13dade0c6f3',
+            # AlphaFold-2.0.0_n-cpu.patch
+            'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',
+            # AlphaFold-ColabFold-2.3.4_fix-scp-path.patch
+            '07bf81f987bc1ab67b7d71121396449289d3ffb499cddb62a135574f2ca7115a',
+            # AlphaFold-2.0.1_setup_rm_tfcpu.patch
+            '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac',
+            # AlphaFold-2.3.1_use_openmm_7.7.0.patch
+            'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec',
+        ],
+        'start_dir': 'alphafold-%s' % _commit,
+        'use_pip': True,
+    }),
+]
+
+use_pip = True
+
+exts_list = [
+    ('PDBFixer', '1.8.1', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'],
+    }),
+    ('toolz', '0.12.0', {
+        'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
+    }),
+    ('chex', '0.1.6', {
+        'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'],
+    }),
+    ('tabulate', '0.9.0', {
+        'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'],
+    }),
+    ('jmp', '0.0.4', {
+        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+    }),
+    ('dm-haiku', '0.0.9', {
+        'modulename': 'haiku',
+        'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'],
+    }),
+    ('dm-tree', '0.1.8', {
+        'modulename': 'tree',
+        'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'],
+    }),
+    ('websocket-client', '1.5.1', {
+        'modulename': 'websocket',
+        'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'],
+    }),
+    ('docker', '6.0.1', {
+        'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'],
+    }),
+    ('immutabledict', '2.2.3', {
+        'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+_alphafold_buildir = '%%(builddir)s/%%(namelower)s-%s' % _commit
+
+postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    # run_alphafold.py script is missing a shebang...
+    "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
+    "cat %s/run_alphafold.py >> %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir,
+    "chmod a+x %(installdir)s/bin/run_alphafold*.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir,
+    "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
+    # run tests for run_alphafold.py script;
+    # shouldn't do this in sanity check to avoid breaking use of --module-only
+    "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH "
+    "python %s/run_alphafold_test.py" % _alphafold_buildir,
+]
+
+sanity_check_paths = {
+    'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
+}
+
+sanity_check_commands = [
+    "pdbfixer --help",
+    "python -m openmm.testInstallation",
+    "python -c 'import alphafold'",
+    "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
+]
+
+sanity_pip_check = True
+
+# these allow to make predictions on proteins that would typically be too long to fit into GPU memory;
+# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py
+modextravars = {
+    'TF_FORCE_UNIFIED_MEMORY': '1',
+    'XLA_PYTHON_CLIENT_MEM_FRACTION': '3',
+    'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1',
+    'OPENMM_RELAX': 'CUDA'  # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb
new file mode 100644
index 00000000000..9297ff62b97
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb
@@ -0,0 +1,167 @@
+easyblock = 'PythonBundle'
+
+name = 'AlphaFold'
+version = '2.3.4'
+versionsuffix = '-ColabFold'
+_commit = '41807ea2c75706cf03f790f06ca191dc04331e41'
+
+homepage = 'https://github.com/sokrypton/alphafold'
+description = """
+AlphaFold can predict protein structures with atomic accuracy even where no
+similar structure is known.
+This package of AlphaFold contains patches for ColabFold."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    # required for installing dm-tree
+    ('Bazel', '5.1.1'),
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('PyYAML', '6.0'),
+    ('TensorFlow', '2.11.0'),
+    ('Biopython', '1.79'),
+    ('HH-suite', '3.3.0'),
+    ('HMMER', '3.3.2'),
+    ('Kalign', '3.3.5'),
+    ('jax', '0.3.25'),  # also provides absl-py
+    ('OpenMM', '8.0.0'),
+]
+
+# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common,
+# see docker/Dockerfile in AlphaFold repository
+local_scp_commit = '7102c6'
+
+components = [
+    (name, version, {
+        'easyblock': 'PythonPackage',
+        'source_urls': [
+            'https://github.com/sokrypton/alphafold/archive/',
+            'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit,
+        ],
+        'sources': [
+            {
+                'download_filename': '%s.tar.gz' % _commit,
+                'filename': '%s-%s.tar.gz' % (name.lower() + versionsuffix.lower(), version)
+            },
+            {
+                'download_filename': 'stereo_chemical_props.txt',
+                'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit,
+                'extract_cmd': "cp %s .",
+            },
+        ],
+        'patches': [
+            'AlphaFold-ColabFold-2.3.4_data-dep-paths.patch',
+            'AlphaFold-2.0.0_n-cpu.patch',
+            'AlphaFold-ColabFold-2.3.4_fix-scp-path.patch',
+            'AlphaFold-2.0.1_setup_rm_tfcpu.patch',
+            'AlphaFold-2.3.1_use_openmm_7.7.0.patch',
+        ],
+        'checksums': [
+            'be6778333fc110b8662b0e262798d6fc1663a14d9341469c6558b2d7771b8024',  # alphafold-colabfold-2.3.4.tar.gz
+            '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451',  # stereo_chemical_props-7102c6.txt
+            # AlphaFold-ColabFold-2.3.4_data-dep-paths.patch
+            '3826e357c35a58b2c8c0fab41ac8ae1b4d4c135162fe47ded577a13dade0c6f3',
+            # AlphaFold-2.0.0_n-cpu.patch
+            'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04',
+            # AlphaFold-ColabFold-2.3.4_fix-scp-path.patch
+            '07bf81f987bc1ab67b7d71121396449289d3ffb499cddb62a135574f2ca7115a',
+            # AlphaFold-2.0.1_setup_rm_tfcpu.patch
+            '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac',
+            # AlphaFold-2.3.1_use_openmm_7.7.0.patch
+            'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec',
+        ],
+        'start_dir': 'alphafold-%s' % _commit,
+        'use_pip': True,
+    }),
+]
+
+use_pip = True
+
+exts_list = [
+    ('PDBFixer', '1.8.1', {
+        'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'],
+    }),
+    ('toolz', '0.12.0', {
+        'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'],
+    }),
+    ('chex', '0.1.6', {
+        'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'],
+    }),
+    ('tabulate', '0.9.0', {
+        'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'],
+    }),
+    ('jmp', '0.0.4', {
+        'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'],
+    }),
+    ('dm-haiku', '0.0.9', {
+        'modulename': 'haiku',
+        'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'],
+    }),
+    ('dm-tree', '0.1.8', {
+        'modulename': 'tree',
+        'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'],
+    }),
+    ('websocket-client', '1.5.1', {
+        'modulename': 'websocket',
+        'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'],
+    }),
+    ('docker', '6.0.1', {
+        'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'],
+    }),
+    ('immutabledict', '2.2.3', {
+        'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'],
+    }),
+    ('contextlib2', '21.6.0', {
+        'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'],
+    }),
+    ('ml_collections', '0.1.1', {
+        'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ",
+        'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'],
+    }),
+]
+
+_alphafold_buildir = '%%(builddir)s/%%(namelower)s-%s' % _commit
+
+postinstallcmds = [
+    "mkdir -p %(installdir)s/bin",
+    # run_alphafold.py script is missing a shebang...
+    "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py",
+    "cat %s/run_alphafold.py >> %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir,
+    "chmod a+x %(installdir)s/bin/run_alphafold*.py",
+    "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold",
+    "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir,
+    "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit,
+    # run tests for run_alphafold.py script;
+    # shouldn't do this in sanity check to avoid breaking use of --module-only
+    "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH "
+    "python %s/run_alphafold_test.py" % _alphafold_buildir,
+]
+
+sanity_check_paths = {
+    'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'],
+}
+
+sanity_check_commands = [
+    "pdbfixer --help",
+    "python -m openmm.testInstallation",
+    "python -c 'import alphafold'",
+    "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'",
+]
+
+sanity_pip_check = True
+
+modextravars = {
+    'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1',
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch
new file mode 100644
index 00000000000..388d7aa02d2
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch
@@ -0,0 +1,134 @@
+pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data
+(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py);
+pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild
+author: Kenneth Hoste (HPC-UGent)
+--- run_alphafold.py.orig	2023-02-18 15:59:05.000000000 +0100
++++ run_alphafold.py	2023-04-17 13:54:08.910029182 +0200
+@@ -42,6 +42,46 @@
+ import numpy as np
+ 
+ # Internal import (7716).
++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:])
++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:])
++
++data_dir = os.getenv('ALPHAFOLD_DATA_DIR')
++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA'
++
++if data_dir:
++    mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa')
++    uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta')
++    template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files')
++    obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat')
++    if use_monomer_preset:
++        pdb_seqres_database_path = None
++        uniprot_database_path = None
++        pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70')
++    else:
++        pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt')
++        uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta')
++        pdb70_database_path = None
++    if use_reduced_dbs:
++        small_bfd_database_path =  os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta')
++        uniref30_database_path = None 
++        bfd_database_path = None 
++    else:
++        small_bfd_database_path = None 
++        bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt')
++        uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_2021_03')
++else:
++    sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!")
++    uniref90_database_path = None
++    mgnify_database_path = None
++    bfd_database_path = None
++    uniref30_database_path = None
++    pdb70_database_path = None
++    template_mmcif_dir = None
++    obsolete_pdbs_path = None
++    small_bfd_database_path = None
++    uniprot_database_path = None
++    pdb_seqres_database_path = None 
++    use_gpu_relax = None
+ 
+ logging.set_verbosity(logging.INFO)
+ 
+@@ -59,7 +99,7 @@
+     'separated by commas. All FASTA paths must have a unique basename as the '
+     'basename is used to name the output directories for each prediction.')
+ 
+-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.')
++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.')
+ flags.DEFINE_string('output_dir', None, 'Path to a directory that will '
+                     'store the results.')
+ flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'),
+@@ -74,27 +114,27 @@
+                     'Path to the hmmbuild executable.')
+ flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'),
+                     'Path to the Kalign executable.')
+-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 '
++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 '
+                     'database for use by JackHMMER.')
+-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify '
++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify '
+                     'database for use by JackHMMER.')
+-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD '
++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD '
+                     'database for use by HHblits.')
+-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small '
++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small '
+                     'version of BFD used with the "reduced_dbs" preset.')
+-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 '
++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 '
+                     'database for use by HHblits.')
+-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot '
++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot '
+                     'database for use by JackHMMer.')
+-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 '
++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 '
+                     'database for use by HHsearch.')
+-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB '
++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB '
+                     'seqres database for use by hmmsearch.')
+-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with '
++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with '
+                     'template mmCIF structures, each named <pdb_id>.cif')
+ flags.DEFINE_string('max_template_date', None, 'Maximum template release date '
+                     'to consider. Important if folding historical test sets.')
+-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a '
++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a '
+                     'mapping from obsolete PDB IDs to the PDB IDs of their '
+                     'replacements.')
+ flags.DEFINE_enum('db_preset', 'full_dbs',
+@@ -137,7 +177,7 @@
+                         'distracting stereochemical violations but might help '
+                         'in case you are having issues with the relaxation '
+                         'stage.')
+-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. '
++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. '
+                      'Relax on GPU can be much faster than CPU, so it is '
+                      'recommended to enable if possible. GPUs must be available'
+                      ' if this setting is enabled.')
+@@ -334,6 +374,10 @@
+                        'sure it is installed on your system.')
+ 
+   use_small_bfd = FLAGS.db_preset == 'reduced_dbs'
++  if use_small_bfd and data_dir:
++    bfd_database_path = None
++    uniref30_database_path = None
++  
+   _check_flag('small_bfd_database_path', 'db_preset',
+               should_be_set=use_small_bfd)
+   _check_flag('bfd_database_path', 'db_preset',
+@@ -456,13 +500,7 @@
+   flags.mark_flags_as_required([
+       'fasta_paths',
+       'output_dir',
+-      'data_dir',
+-      'uniref90_database_path',
+-      'mgnify_database_path',
+-      'template_mmcif_dir',
+       'max_template_date',
+-      'obsolete_pdbs_path',
+-      'use_gpu_relax',
+   ])
+ 
+   app.run(main)
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch
new file mode 100644
index 00000000000..0714243785e
--- /dev/null
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch
@@ -0,0 +1,14 @@
+fix path to stereo_chemical_props.txt when AlphaFold is installed with EasyBuild
+author: Kenneth Hoste (HPC-UGent)
+update 2.0.0 -> 2.1.0: Thomas Hoffmann (EMBL Heidelberg)
+--- alphafold/common/residue_constants.py.orig	2023-04-17 13:59:57.535153646 +0200
++++ alphafold/common/residue_constants.py	2023-04-17 14:02:33.555747657 +0200
+@@ -25,7 +25,7 @@
+ # Internal import (35fd).
+ 
+ from . import __file__ 
+-stereo_chemical_props_path = os.path.join(os.path.dirname(__file__), f'stereo_chemical_props.txt')  
++stereo_chemical_props_path = os.path.join(os.getenv('EBROOTALPHAFOLD', 'alphafold/common'), 'stereo_chemical_props.txt')
+ 
+ # Distance from one CA to next CA [trans configuration: omega = 180].
+ ca_ca = 3.80209737096
diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..8d8017276a6
--- /dev/null
+++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,58 @@
+easyblock = 'PythonBundle'
+
+name = 'ColabFold'
+version = '1.5.2'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/sokrypton/ColabFold'
+description = """Making protein folding accessible to all. Predict proteins structures both in
+google colab and on your machine."""
+github_account = 'sokrypton'
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('AlphaFold', '2.3.4', versionsuffix + '-%(name)s'),
+    ('matplotlib', '3.5.2'),
+    ('tqdm', '4.64.0'),
+    ('py3Dmol', '2.0.1.post1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('colabfold', version, {
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'],
+        # fix requirement on Python 3.10.x revisions and TensorFlow
+        'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&",
+        'use_pip_extras': 'alphafold',
+    }),
+]
+
+postinstallcmds = [
+    # Copy notebooks to installation directory
+    "mkdir %(installdir)s/notebooks",
+    "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/",
+]
+
+sanity_check_paths = {
+    'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'],
+}
+
+sanity_check_commands = [
+    "colabfold_batch --help",
+]
+
+sanity_pip_check = True
+
+modloadmsg = """
+%(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks
+"""
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb
new file mode 100644
index 00000000000..c8ebee84c19
--- /dev/null
+++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb
@@ -0,0 +1,56 @@
+easyblock = 'PythonBundle'
+
+name = 'ColabFold'
+version = '1.5.2'
+
+homepage = 'https://github.com/sokrypton/ColabFold'
+description = """Making protein folding accessible to all. Predict proteins structures both in
+google colab and on your machine."""
+github_account = 'sokrypton'
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('AlphaFold', '2.3.4', '-%(name)s'),
+    ('matplotlib', '3.5.2'),
+    ('tqdm', '4.64.0'),
+    ('py3Dmol', '2.0.1.post1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('colabfold', version, {
+        'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'],
+        # fix requirement on Python 3.10.x revisions and TensorFlow
+        'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&",
+        'use_pip_extras': 'alphafold',
+    }),
+]
+
+postinstallcmds = [
+    # Copy notebooks to installation directory
+    "mkdir %(installdir)s/notebooks",
+    "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/",
+]
+
+sanity_check_paths = {
+    'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'],
+}
+
+sanity_check_commands = [
+    "colabfold_batch --help",
+]
+
+sanity_pip_check = True
+
+modloadmsg = """
+%(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks
+"""
+
+moduleclass = 'bio'

From 67ba82f1331e1305932cdfcabeb686b3dca43a18 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 18 Apr 2023 14:58:22 +0200
Subject: [PATCH 370/601] comment out ALPHAFOLD_DATA_DIR in AlphaFold-ColabFold
 v2.3.4

---
 .../AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb         | 2 +-
 .../a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb
index 51dbe4220f7..0842216c4e9 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb
@@ -171,7 +171,7 @@ sanity_pip_check = True
 modextravars = {
     'TF_FORCE_UNIFIED_MEMORY': '1',
     'XLA_PYTHON_CLIENT_MEM_FRACTION': '3',
-    'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1',
+    # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs',  # please adapt,
     'OPENMM_RELAX': 'CUDA'  # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189
 }
 
diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb
index 9297ff62b97..614a7fe1e6e 100644
--- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb
+++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb
@@ -161,7 +161,7 @@ sanity_check_commands = [
 sanity_pip_check = True
 
 modextravars = {
-    'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1',
+    # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs',  # please adapt
 }
 
 moduleclass = 'bio'

From fca88c0dcd2143012c584ada7377ddbd5c65d248 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 18 Apr 2023 15:30:07 +0200
Subject: [PATCH 371/601] adding easyconfigs:
 py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb

---
 .../py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb     | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..de2808866ae
--- /dev/null
+++ b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonBundle'
+
+name = 'py3Dmol'
+version = '2.0.1.post1'
+
+homepage = 'https://github.com/3dmol/3Dmol.js/tree/master/py3Dmol'
+description = "A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook."
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('IPython', '8.5.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'modulename': '%(name)s',
+        'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'vis'

From db5a46bb9e693aa6597107dbb800b2109fc1a7aa Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 18 Apr 2023 15:49:37 +0200
Subject: [PATCH 372/601] add build dependency on binutils to py3Dmol
 v2.0.1.post1

---
 .../p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb           | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb
index de2808866ae..9e22b8a26a6 100644
--- a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb
@@ -8,6 +8,10 @@ description = "A simple IPython/Jupyter widget to embed an interactive 3Dmol.js
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
 dependencies = [
     ('Python', '3.10.4'),
     ('IPython', '8.5.0'),

From f945c4323074659aa89562981551d39f0538bce3 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 18 Apr 2023 16:38:22 +0100
Subject: [PATCH 373/601] adding easyconfigs: FUSE-3.14.1-foss-2022a.eb

---
 .../f/FUSE/FUSE-3.14.1-foss-2022a.eb          | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb
new file mode 100644
index 00000000000..8f0af720ccd
--- /dev/null
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb
@@ -0,0 +1,29 @@
+easyblock = 'MesonNinja'
+
+name = 'FUSE'
+version = '3.14.1'
+
+homepage = 'https://github.com/libfuse/libfuse'
+description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20']
+
+builddependencies = [
+    ('Meson', '0.62.1'),
+    ('Ninja', '1.10.2'),
+]
+
+# -Dutils=True only works as root 
+configopts = '-Dutils=False'
+
+sanity_check_paths = {
+    'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT,
+              'lib64/pkgconfig/fuse%(version_major)s.pc'],
+    'dirs': ['include/fuse%(version_major)s'],
+}
+
+moduleclass = 'lib'

From c27be343ee6fbdaeb5999c7f1a8211d2591d858e Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 18 Apr 2023 11:41:34 -0700
Subject: [PATCH 374/601] {bio}[SYSTEM] IgBlast 1.21.0 update

---
 .../i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb     | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb

diff --git a/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb
new file mode 100644
index 00000000000..8d3bf7d2572
--- /dev/null
+++ b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb
@@ -0,0 +1,30 @@
+# Easybuild Easyconfig
+#
+# John Dey <jfdey@fredhutch.org>
+#
+# Fred Hutchinson Cancer Center - Seattle Washington
+easyblock = "Tarball"
+
+name = 'IgBLAST'
+version = '1.21.0'
+versionsuffix = '-x64-linux'
+
+homepage = 'https://ncbi.github.io/igblast'
+description = """IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences."""
+
+toolchain = SYSTEM
+
+source_urls = ['ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/%(version)s']
+sources = ['ncbi-%(namelower)s-%(version)s-x64-linux.tar.gz']
+checksums = ['737d19aed8f3d8d717fcd8a2fa22e93b0830dd9cced729f41a67df95c8aef136']
+
+sanity_check_paths = {
+    'files': ["bin/igblastn", 'bin/igblastp'],
+    'dirs': ['bin']
+}
+
+sanity_check_commands = ['%(namelower)sn -h']
+
+modextravars = {'IGDATA': '%(installdir)s/internal_data'}
+
+moduleclass = 'bio'

From d12b3630f3503af1dbad8679dc14ef956464fc9f Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Tue, 18 Apr 2023 21:48:51 +0100
Subject: [PATCH 375/601] Patchfile from PR #16110 used as identical

---
 .../s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb           |   4 +-
 .../SLiM-4.0.1_use_external_zlib_gsl.patch    | 161 ------------------
 2 files changed, 2 insertions(+), 163 deletions(-)
 delete mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch

diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb
index 4d9a4c39ed5..496b738e7b5 100644
--- a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb
@@ -12,11 +12,11 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'}
 source_urls = ['https://github.com/MesserLab/%(name)s/archive']
 sources = ['v%(version)s.tar.gz']
 patches = [
-    '%(name)s-%(version)s_use_external_zlib_gsl.patch',
+    '%(name)s-4.0_use_external_zlib_gsl.patch',
 ]
 checksums = [
     {'v4.0.1.tar.gz': 'a44564023db372cd438b4e6c729a4ba59200d1217a63b3694ca7903436886cc2'},
-    {'SLiM-4.0.1_use_external_zlib_gsl.patch': '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755'},
+    {'SLiM-4.0_use_external_zlib_gsl.patch': '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755'},
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch
deleted file mode 100644
index 894f69dd4f3..00000000000
--- a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch
+++ /dev/null
@@ -1,161 +0,0 @@
-commit 2ba4892b9327e5d21fdd712e178447d2ecd3665a
-Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
-Date:   Wed Aug 24 08:15:39 2022 +0200
-
-    Use external Zlib and GSL instead of internal ones.
-    And use correctly names zlib functions.
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 487c7bcd..0aae03ea 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -157,18 +157,20 @@ endif()
- #endif()
- 
- # GSL 
--set(TARGET_NAME gsl)
--file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c)
--set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg)
--add_library(${TARGET_NAME} STATIC ${GSL_SOURCES})
--target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES})
-+# Use external GSL instead
-+#set(TARGET_NAME gsl)
-+#file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c)
-+#set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg)
-+#add_library(${TARGET_NAME} STATIC ${GSL_SOURCES})
-+#target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES})
- 
- # ZLIB
--set(TARGET_NAME eidos_zlib)
--file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c)
--set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib)
--add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES})
--target_include_directories(${TARGET_NAME} PUBLIC)
-+# Use external Zlib instead
-+#set(TARGET_NAME eidos_zlib)
-+#file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c)
-+#set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib)
-+#add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES})
-+#target_include_directories(${TARGET_NAME} PUBLIC)
- 
- # KASTORE
- set(TARGET_NAME kastore)
-@@ -198,7 +200,7 @@ list(APPEND SLIM_SOURCES "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" ${PROJECT_SOU
- 
- add_executable(${TARGET_NAME} ${SLIM_SOURCES})
- target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/eidos")
--target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables)
-+target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables)
- if(WIN32)
-     set_source_files_properties(${SLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
-     set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
-@@ -211,7 +213,7 @@ set(TARGET_NAME eidos)
- file(GLOB_RECURSE EIDOS_SOURCES  ${PROJECT_SOURCE_DIR}/eidos/*.cpp  ${PROJECT_SOURCE_DIR}/eidostool/*.cpp)
- add_executable(${TARGET_NAME} ${EIDOS_SOURCES})
- target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/eidos")
--target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables)
-+target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables)
- if(WIN32)
-     set_source_files_properties(${EIDOS_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
-     set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
-@@ -244,15 +246,15 @@ set_target_properties( ${TARGET_NAME} PROPERTIES LINKER_LANGUAGE CXX)
- target_compile_definitions( ${TARGET_NAME} PRIVATE EIDOSGUI=1 SLIMGUI=1)
- target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore")
- if(APPLE)
--	target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib /usr/lib/libobjc.A.dylib )
-+	target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z /usr/lib/libobjc.A.dylib )
- else()
-     if(WIN32)
-         set_source_files_properties(${QTSLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h")
-         set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos SLiMgui PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib")
-         target_include_directories(${TARGET_NAME} BEFORE PUBLIC ${GNU_DIR})
--        target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib gnu )
-+        target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z gnu )
-     else()
--	    target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib )
-+	    target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z )
-     endif()
- endif()
- install(TARGETS ${TARGET_NAME} DESTINATION bin)
-diff --git a/eidos/eidos_functions.cpp b/eidos/eidos_functions.cpp
-index 4f52c763..ac9de199 100644
---- a/eidos/eidos_functions.cpp
-+++ b/eidos/eidos_functions.cpp
-@@ -55,11 +55,11 @@
- 
- #include "string.h"
- 
--#include "gsl_linalg.h"
--#include "gsl_errno.h"
--#include "gsl_cdf.h"
-+#include <gsl/gsl_linalg.h>
-+#include <gsl/gsl_errno.h>
-+#include <gsl/gsl_cdf.h>
- 
--#include "../eidos_zlib/zlib.h"
-+#include <zlib.h>
- 
- #include "eidos_globals.h"
- #if EIDOS_ROBIN_HOOD_HASHING
-@@ -11475,7 +11475,7 @@ EidosValue_SP Eidos_ExecuteFunction_writeTempFile(const std::vector<EidosValue_S
- 	if (do_compress)
- 	{
- 		// compression using zlib; very different from the no-compression case, unfortunately, because here we use C-based APIs
--		gzFile gzf = z_gzdopen(fd, "wb");
-+		gzFile gzf = gzdopen(fd, "wb");
- 		
- 		if (!gzf)
- 		{
-diff --git a/eidos/eidos_globals.cpp b/eidos/eidos_globals.cpp
-index dc801c2f..95984159 100644
---- a/eidos/eidos_globals.cpp
-+++ b/eidos/eidos_globals.cpp
-@@ -65,13 +65,13 @@
- #endif
- 
- // for Eidos_WelchTTest()
--#include "gsl_cdf.h"
-+#include <gsl/gsl_cdf.h>
- 
- // for Eidos_calc_sha_256()
- #include <stdint.h>
- 
- // for _Eidos_FlushZipBuffer()
--#include "../eidos_zlib/zlib.h"
-+#include <zlib.h>
- 
- // for Eidos_ColorPaletteLookup()
- #include "eidos_tinycolormap.h"
-@@ -1570,7 +1570,7 @@ bool _Eidos_FlushZipBuffer(const std::string &file_path, const std::string &outs
- {
- 	//std::cout << "_Eidos_FlushZipBuffer() called for " << file_path << std::endl;
- 	
--	gzFile gzf = z_gzopen(file_path.c_str(), "ab");
-+	gzFile gzf = gzopen(file_path.c_str(), "ab");
- 	
- 	if (!gzf)
- 		return false;
-@@ -1678,7 +1678,7 @@ void Eidos_WriteToFile(const std::string &p_file_path, std::vector<const std::st
- 		{
- 			// this code can handle both the append and the non-append case, but the append case may generate very low-quality
- 			// compression (potentially even worse than the uncompressed data) due to having an excess of gzip headers
--			gzFile gzf = z_gzopen(p_file_path.c_str(), p_append ? "ab" : "wb");
-+			gzFile gzf = gzopen(p_file_path.c_str(), p_append ? "ab" : "wb");
- 			
- 			if (!gzf)
- 				EIDOS_TERMINATION << "#ERROR (Eidos_WriteToFile): could not write to file at path " << p_file_path << "." << EidosTerminate(nullptr);
-diff --git a/eidos/eidos_rng.h b/eidos/eidos_rng.h
-index 313f75d7..7ab9db4d 100644
---- a/eidos/eidos_rng.h
-+++ b/eidos/eidos_rng.h
-@@ -29,8 +29,8 @@
- 
- // We have our own private copy of (parts of) the GSL library, so that we don't have link dependencies.
- // See the _README file in the gsl directory for information on the local copy of the GSL included in this project.
--#include "gsl_rng.h"
--#include "gsl_randist.h"
-+#include <gsl/gsl_rng.h>
-+#include <gsl/gsl_randist.h>
- 
- #include <stdint.h>
- #include <cmath>

From 8c6dac0ebc9e9b9ed275d6867cf7dc9d4e00f2bd Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 19 Apr 2023 14:45:32 +0100
Subject: [PATCH 376/601] adding easyconfigs: FUSE-3.14.1-foss-2022b.eb

---
 .../f/FUSE/FUSE-3.14.1-foss-2022b.eb          | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb
new file mode 100644
index 00000000000..54ea701e95e
--- /dev/null
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb
@@ -0,0 +1,29 @@
+easyblock = 'MesonNinja'
+
+name = 'FUSE'
+version = '3.14.1'
+
+homepage = 'https://github.com/libfuse/libfuse'
+description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20']
+
+builddependencies = [
+    ('Meson', '0.64.0'),
+    ('Ninja', '1.11.1'),
+]
+
+# -Dutils=True only works as root 
+configopts = '-Dutils=False'
+
+sanity_check_paths = {
+    'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT,
+              'lib64/pkgconfig/fuse%(version_major)s.pc'],
+    'dirs': ['include/fuse%(version_major)s'],
+}
+
+moduleclass = 'lib'

From 213cb0ba7beb248426b29ec928dccec4e42a716d Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Wed, 19 Apr 2023 16:49:44 +0200
Subject: [PATCH 377/601] adding easyconfigs: GCC-13.0.1.eb, GCCcore-13.0.1.eb,
 binutils-2.40.eb, binutils-2.40-GCCcore-13.0.1.eb,
 Bison-3.8.2-GCCcore-13.0.1.eb, flex-2.6.4-GCCcore-13.0.1.eb,
 help2man-1.49.3-GCCcore-13.0.1.eb, M4-1.4.19-GCCcore-13.0.1.eb,
 zlib-1.2.13.eb, zlib-1.2.13-GCCcore-13.0.1.eb

---
 .../b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb     | 28 ++++++++
 .../binutils/binutils-2.40-GCCcore-13.0.1.eb  | 31 +++++++++
 .../easyconfigs/b/binutils/binutils-2.40.eb   | 26 +++++++
 .../f/flex/flex-2.6.4-GCCcore-13.0.1.eb       | 34 ++++++++++
 easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb     | 22 ++++++
 .../easyconfigs/g/GCCcore/GCCcore-13.0.1.eb   | 67 +++++++++++++++++++
 .../help2man-1.49.3-GCCcore-13.0.1.eb         | 25 +++++++
 .../m/M4/M4-1.4.19-GCCcore-13.0.1.eb          | 29 ++++++++
 .../z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb      | 30 +++++++++
 easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb   | 32 +++++++++
 10 files changed, 324 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40.eb
 create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb
 create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb

diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb
new file mode 100644
index 00000000000..45f87974dc5
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'Bison'
+version = '3.8.2'
+
+homepage = 'https://www.gnu.org/software/bison'
+description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar
+ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb']
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    # use same binutils version that was used when building GCCcore toolchain
+    ('binutils', '2.39', '', SYSTEM),
+]
+
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')],
+    'dirs': [],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb
new file mode 100644
index 00000000000..36234b61ea1
--- /dev/null
+++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb
@@ -0,0 +1,31 @@
+name = 'binutils'
+version = '2.40'
+
+homepage = 'https://directory.fsf.org/project/binutils/'
+description = "binutils: GNU binary utilities"
+
+toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956']
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils
+    ('binutils', version, '', SYSTEM)
+]
+
+dependencies = [
+    # zlib is a runtime dep to avoid that it gets embedded in libbfd.so,
+    # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350
+    ('zlib', '1.2.13'),
+]
+
+# avoid build failure when makeinfo command is not available
+# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345
+buildopts = 'MAKEINFO=true'
+installopts = buildopts
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40.eb
new file mode 100644
index 00000000000..a04b02ae921
--- /dev/null
+++ b/easybuild/easyconfigs/b/binutils/binutils-2.40.eb
@@ -0,0 +1,26 @@
+name = 'binutils'
+version = '2.40'
+
+homepage = 'https://directory.fsf.org/project/binutils/'
+
+description = "binutils: GNU binary utilities"
+
+toolchain = SYSTEM
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956']
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    # zlib required, but being linked in statically, so not a runtime dep
+    ('zlib', '1.2.13'),
+]
+
+# avoid build failure when makeinfo command is not available
+# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345
+buildopts = 'MAKEINFO=true'
+installopts = buildopts
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb
new file mode 100644
index 00000000000..e4b6d071111
--- /dev/null
+++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb
@@ -0,0 +1,34 @@
+name = 'flex'
+version = '2.6.4'
+
+homepage = 'http://flex.sourceforge.net/'
+
+description = """
+ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,
+ sometimes called a tokenizer, is a program which recognizes lexical patterns
+ in text.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995']
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('help2man', '1.49.3'),
+    # use same binutils version that was used when building GCC toolchain
+    ('binutils', '2.39', '', SYSTEM),
+]
+
+dependencies = [
+    ('M4', '1.4.19'),
+]
+
+# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct
+# header, see https://github.com/westes/flex/issues/241
+preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && '
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb b/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb
new file mode 100644
index 00000000000..b9c224ad66e
--- /dev/null
+++ b/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb
@@ -0,0 +1,22 @@
+easyblock = 'Bundle'
+
+name = 'GCC'
+version = '13.0.1'
+
+homepage = 'https://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = SYSTEM
+
+dependencies = [
+    ('GCCcore', version),
+    # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain)
+    ('binutils', '2.40', '', ('GCCcore', version)),
+]
+
+altroot = 'GCCcore'
+altversion = 'GCCcore'
+
+# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS)
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb
new file mode 100644
index 00000000000..0b8d30d3782
--- /dev/null
+++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb
@@ -0,0 +1,67 @@
+easyblock = 'EB_GCC'
+
+name = 'GCCcore'
+version = '13.0.1'
+
+homepage = 'https://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = SYSTEM
+
+source_urls = [
+    'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s',  # GCC auto-resolving HTTP mirror
+    'https://sourceware.org/pub/gcc/releases/gcc-%(version)s',  # fallback URL for GCC
+    'https://ftpmirror.gnu.org/gnu/gmp',  # idem for GMP
+    'https://ftpmirror.gnu.org/gnu/mpfr',  # idem for MPFR
+    'https://ftpmirror.gnu.org/gnu/mpc',  # idem for MPC
+    'ftp://gcc.gnu.org/pub/gcc/infrastructure/',  # GCC dependencies
+    'https://gcc.gnu.org/pub/gcc/infrastructure/',  # HTTPS mirror for GCC dependencies
+    'https://libisl.sourceforge.io/',  # fallback URL for isl
+    'https://sourceware.org/pub/newlib/',  # for newlib
+    'https://github.com/MentorEmbedded/nvptx-tools/archive',  # for nvptx-tools
+]
+sources = [
+    {
+        'source_urls': ['https://gcc.gnu.org/pub/gcc/snapshots/13.1.0-RC2-20230419/'],
+        'filename': 'gcc-13.1.0-RC2-20230419.tar.gz',
+    },
+    # 'gcc-%(version)s.tar.gz',
+    'gmp-6.2.1.tar.bz2',
+    'mpfr-4.1.0.tar.bz2',
+    'mpc-1.2.1.tar.gz',
+    'isl-0.24.tar.bz2',
+    'newlib-4.1.0.tar.gz',
+    {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'},
+]
+patches = [
+    'GCCcore-6.2.0-fix-find-isl.patch',
+    'GCCcore-9.3.0_gmp-c99.patch',
+]
+checksums = [
+    {'gcc-13.1.0-RC2-20230419.tar.gz': '31188ab89af2b52fc5e3a2ef77c52d4b762e18320b3d741fa947e3d0dd306134'},
+    {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'},
+    {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'},
+    {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'},
+    {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'},
+    {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'},
+    {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'},
+    {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'},
+    {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'},
+]
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    ('binutils', '2.40'),
+]
+
+languages = ['c', 'c++', 'fortran']
+
+withisl = True
+withnvptx = True
+
+# Perl is only required when building with NVPTX support
+if withnvptx:
+    osdependencies = ['perl']
+
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb
new file mode 100644
index 00000000000..92adccec4f1
--- /dev/null
+++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'help2man'
+version = '1.49.3'
+
+homepage = 'https://www.gnu.org/software/help2man/'
+description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_XZ]
+checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f']
+
+builddependencies = [
+    # use same binutils version that was used when building GCC toolchain
+    ('binutils', '2.40', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['bin/help2man'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb
new file mode 100644
index 00000000000..6a458ba47b3
--- /dev/null
+++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'M4'
+version = '1.4.19'
+
+homepage = 'https://www.gnu.org/software/m4/m4.html'
+description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible
+  although it has some extensions (for example, handling more than 9 positional parameters to macros).
+ GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70']
+
+# use same binutils version that was used when building GCC toolchain
+builddependencies = [('binutils', '2.39', '', SYSTEM)]
+
+# '-fgnu89-inline' is required to avoid linking errors with older glibc's,
+# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529
+configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline"
+
+sanity_check_paths = {
+    'files': ['bin/m4'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb
new file mode 100644
index 00000000000..32d9c8ca56c
--- /dev/null
+++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'zlib'
+version = '1.2.13'
+
+homepage = 'https://www.zlib.net/'
+description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is,
+ not covered by any patents -- lossless data-compression library for use on virtually any
+ computer hardware and operating system."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://zlib.net/fossils']
+sources = [SOURCELOWER_TAR_GZ]
+# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch']
+checksums = [
+    'b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30',  # zlib-1.2.12.tar.gz
+    # 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238',  # zlib-1.2.12_fix-CC-logic-in-configure.patch
+]
+
+# use same binutils version that was used when building GCC toolchain
+builddependencies = [('binutils', '2.40', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb
new file mode 100644
index 00000000000..397dbe63b57
--- /dev/null
+++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'zlib'
+version = '1.2.13'
+
+homepage = 'https://www.zlib.net/'
+
+description = """
+ zlib is designed to be a free, general-purpose, legally unencumbered -- that
+ is, not covered by any patents -- lossless data-compression library for use
+ on virtually any computer hardware and operating system.
+"""
+
+toolchain = SYSTEM
+toolchainopts = {'pic': True}
+
+source_urls = ['https://zlib.net/fossils/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30']
+
+# need to take care of $CFLAGS ourselves with dummy toolchain
+# we need to add -fPIC, but should also include -O* option to avoid
+# compiling with -O0 (default for GCC)
+buildopts = 'CFLAGS="-O2 -fPIC"'
+
+sanity_check_paths = {
+    'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a',
+              'lib/libz.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From d50486411c5bda609b36e944587ea4058e90343d Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 19 Apr 2023 17:40:21 +0100
Subject: [PATCH 378/601] Demoted to GCCcore

---
 ...{FUSE-3.14.1-foss-2022b.eb => FUSE-3.14.1-GCCcore-12.2.0.eb} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename easybuild/easyconfigs/f/FUSE/{FUSE-3.14.1-foss-2022b.eb => FUSE-3.14.1-GCCcore-12.2.0.eb} (93%)

diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
similarity index 93%
rename from easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb
rename to easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
index 54ea701e95e..a71b0002a5c 100644
--- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
@@ -6,7 +6,7 @@ version = '3.14.1'
 homepage = 'https://github.com/libfuse/libfuse'
 description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface"
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 
 source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/']
 sources = [SOURCELOWER_TAR_XZ]

From c98853bc01ae507eecf03939a74a4cd968808409 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?=
 <43338785+sassy-crick@users.noreply.github.com>
Date: Wed, 19 Apr 2023 20:09:04 +0100
Subject: [PATCH 379/601] Update FUSE-3.14.1-GCCcore-12.2.0.eb

Binutils added
---
 easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
index a71b0002a5c..1be42749206 100644
--- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb
@@ -15,6 +15,7 @@ checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20']
 builddependencies = [
     ('Meson', '0.64.0'),
     ('Ninja', '1.11.1'),
+    ('binutils', '2.39')
 ]
 
 # -Dutils=True only works as root 

From 32183c4fcf8090d6a762e4e2c4f64df53fc5cd09 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 19 Apr 2023 21:14:05 +0100
Subject: [PATCH 380/601] Demoted from foss to GCCcore, as done in PR #17759

---
 ...FUSE-3.14.1-foss-2022a.eb => FUSE-3.14.1-GCCcore-11.3.0.eb} | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)
 rename easybuild/easyconfigs/f/FUSE/{FUSE-3.14.1-foss-2022a.eb => FUSE-3.14.1-GCCcore-11.3.0.eb} (90%)

diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
similarity index 90%
rename from easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb
rename to easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
index 8f0af720ccd..e917f49a009 100644
--- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
@@ -6,7 +6,7 @@ version = '3.14.1'
 homepage = 'https://github.com/libfuse/libfuse'
 description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface"
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
 source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/']
 sources = [SOURCELOWER_TAR_XZ]
@@ -15,6 +15,7 @@ checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20']
 builddependencies = [
     ('Meson', '0.62.1'),
     ('Ninja', '1.10.2'),
+    ('binutils','2.38'),
 ]
 
 # -Dutils=True only works as root 

From bf6ea38cb1f914021e7bede65b05ddec0a6da6c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?=
 <43338785+sassy-crick@users.noreply.github.com>
Date: Wed, 19 Apr 2023 22:02:10 +0100
Subject: [PATCH 381/601] Whitespace corrected

---
 easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
index e917f49a009..856159422b1 100644
--- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb
@@ -15,7 +15,7 @@ checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20']
 builddependencies = [
     ('Meson', '0.62.1'),
     ('Ninja', '1.10.2'),
-    ('binutils','2.38'),
+    ('binutils', '2.38'),
 ]
 
 # -Dutils=True only works as root 

From 88a819d1d5696443caffd6f1f158a3a9f4fd49d8 Mon Sep 17 00:00:00 2001
From: Wendar Lin <wdlin@csie.nctu.edu.tw>
Date: Thu, 20 Apr 2023 18:50:46 +0800
Subject: [PATCH 382/601] add pcre dependency for interproscan

---
 .../i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb          | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb
index d4535511479..aa12f6d8bf5 100644
--- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb
+++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb
@@ -27,6 +27,7 @@ dependencies = [
     ('Perl',    '5.32.1'),
     ('libgd',   '2.3.1'),
     ('Python',  '3.9.5'),
+    ('PCRE',    '8.44'),
 ]
 # NOTE some analyses done by InterProScan require extra tools not included in the interproscan
 # distribution because of license issues.

From 30d858247cfbd826f70617a5e84e01545636d67c Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Thu, 20 Apr 2023 15:57:15 +0200
Subject: [PATCH 383/601] correct the python building of DGL, requires static
 libs

---
 .../easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb
index 9aa9bdcd151..71615bf8576 100644
--- a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb
@@ -103,7 +103,10 @@ _copts = [
 ]
 configopts = ' '.join(_copts)
 
-build_shared_libs = True
+# Must not build shared libs, DGL uses internal versions of, among others, METIS
+# but it doesn't install these internal libraries and simply assumes that everything is
+# statically linked.
+build_shared_libs = False
 
 runtest = 'test'
 
@@ -118,10 +121,9 @@ exts_default_options = {
 
 exts_list = [
     ('dgl', version, {
-        'modulename': False,
         'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
         'start_dir': 'python',
-        'use_pip': False,
+        'installopts': '--use-feature=in-tree-build ',
         'checksums': ['8d26ebb7ed976665bbf5bbd1792d8e6efb13a8fa16e5eb1efed75e07fb982e04'],
     }),
 ]

From d7773dfecde0650884d84ed38deeb63a0a3b8cbc Mon Sep 17 00:00:00 2001
From: "A.H. Kole" <a.h.kole@uu.nl>
Date: Thu, 20 Apr 2023 16:17:57 +0200
Subject: [PATCH 384/601] adding easyconfigs: xmlf90-1.5.6-GCC-11.3.0.eb

---
 .../x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb       | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb
new file mode 100644
index 00000000000..8ec08d98951
--- /dev/null
+++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'xmlf90'
+version = '1.5.6'
+
+homepage = 'https://gitlab.com/siesta-project/libraries/xmlf90'
+description = """A fast XML parser and generator in Fortran"""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://gitlab.com/siesta-project/libraries/xmlf90/-/archive/%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c4492596c911b668b94fee40a53453f06aef3bc41014b9e2f4b51e640ad20528']
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['lib/libxmlf90.a'],
+    'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/xmlf90'],
+}
+
+runtest = 'test'
+
+moduleclass = 'data'

From 641a99f6111a378a5417db192dc32601f9c24c42 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 20 Apr 2023 16:59:14 +0200
Subject: [PATCH 385/601] Only use QE gitlab source url for QE itself

---
 .../QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb  | 10 +++++-----
 .../QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb | 10 +++++-----
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
index 9257514652d..87066c6ae6d 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb
@@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 toolchain = {'name': 'foss', 'version': '2022a'}
 toolchainopts = {'usempi': True, 'openmp': True}
 
-source_urls = [
-    'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s',
-]
 sources = [
     {
         'filename': 'q-e-qe-%(version)s.tar.gz',
         'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_',
+        'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'],
     },
     {
         'filename': 'qe-gipaw-%(version)s.tar.gz',
         'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']
     },
-    {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz',
-     'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']},
+    {
+        'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz',
+        'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']
+    },
 ]
 checksums = [
     'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6',  # q-e-qe-7.1.tar.gz
diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
index e9f90039005..a81be226c25 100644
--- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
+++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb
@@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials
 toolchain = {'name': 'intel', 'version': '2022a'}
 toolchainopts = {'usempi': True, 'openmp': True}
 
-source_urls = [
-    'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s',
-]
 sources = [
     {
         'filename': 'q-e-qe-%(version)s.tar.gz',
         'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_',
+        'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'],
     },
     {
         'filename': 'qe-gipaw-%(version)s.tar.gz',
         'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']
     },
-    {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz',
-     'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']},
+    {
+        'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz',
+        'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']
+    },
 ]
 checksums = [
     'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6',  # q-e-qe-7.1.tar.gz

From bbd111dbc103b6000641acd774e60835778f5dec Mon Sep 17 00:00:00 2001
From: "A.H. Kole" <a.h.kole@uu.nl>
Date: Thu, 20 Apr 2023 17:01:40 +0200
Subject: [PATCH 386/601] adding easyconfigs: libPSML-1.1.12-GCC-11.3.0.eb

---
 .../l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb    | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb
new file mode 100644
index 00000000000..6dba042d193
--- /dev/null
+++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'libPSML'
+version = '1.1.12'
+
+homepage = 'https://gitlab.com/siesta-project/libraries/libpsml'
+description = """A library to handle pseudopotentials in PSML format"""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/-/archive/%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c61503d5a5de119f970f1bf27aa0ac8059b87e81d1a8013bef1bb7993df44c56']
+
+dependencies = [
+    ('xmlf90', '1.5.6'),
+]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['lib/libpsml.a'],
+    'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libpsml'],
+}
+
+runtest = 'test'
+
+moduleclass = 'data'

From 562e6b2fd247e5ad8aef0ff6ec15cbf1c8fbc7d7 Mon Sep 17 00:00:00 2001
From: "A.H. Kole" <a.h.kole@uu.nl>
Date: Thu, 20 Apr 2023 17:40:06 +0200
Subject: [PATCH 387/601] adding easyconfigs: libGridXC-1.1.0-gompi-2022a.eb

---
 .../libGridXC/libGridXC-1.1.0-gompi-2022a.eb  | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
new file mode 100644
index 00000000000..e44041efa6c
--- /dev/null
+++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'libGridXC'
+version = '1.1.0'
+
+homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc'
+description = """A library to compute the exchange and correlation energy
+ and potential in spherical (i.e. atoms) or periodic systems."""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchainopts = {'usempi': True, 'opt': True}
+
+source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/-/archive/%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e7883e57a4db2438ee59437740291c06e0cfe1c8ae1901e4001f32312307e46a']
+
+configopts = "-DWITH_MPI=ON -DWITH_LIBXC=ON"
+
+dependencies = [('libxc', '5.2.3')]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+]
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['lib/libgridxc.a'],
+    'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'],
+}
+
+runtest = 'test'
+
+moduleclass = 'phys'

From ab83b6fbfda8d338033c28d39e97419fcb7ed23a Mon Sep 17 00:00:00 2001
From: Arnold Kole <35299166+ahkole@users.noreply.github.com>
Date: Thu, 20 Apr 2023 21:15:30 +0200
Subject: [PATCH 388/601] Remove explicit setting of default option
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb
index 8ec08d98951..262cfb87e36 100644
--- a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb
@@ -16,8 +16,6 @@ builddependencies = [
     ('CMake', '3.23.1'),
 ]
 
-separate_build_dir = True
-
 sanity_check_paths = {
     'files': ['lib/libxmlf90.a'],
     'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/xmlf90'],

From 357a14ec8805990e2494a755c5cd4d0adad3babd Mon Sep 17 00:00:00 2001
From: Arnold Kole <35299166+ahkole@users.noreply.github.com>
Date: Thu, 20 Apr 2023 21:16:28 +0200
Subject: [PATCH 389/601] Remove explicit setting of default option
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb      | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
index e44041efa6c..1b2f864e5f2 100644
--- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
+++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
@@ -22,8 +22,6 @@ builddependencies = [
     ('CMake', '3.23.1'),
 ]
 
-separate_build_dir = True
-
 sanity_check_paths = {
     'files': ['lib/libgridxc.a'],
     'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'],

From 916e30e2c51aabb143d66075bd865b80b0292ec8 Mon Sep 17 00:00:00 2001
From: rocky_build <rocky_build@rocky7.rocky.bio.utk.edu>
Date: Thu, 20 Apr 2023 15:50:28 -0400
Subject: [PATCH 390/601] adding easyconfigs: BWA-0.7.17-GCCcore-12.2.0.eb

---
 .../b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb        | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..ec08bbe74b1
--- /dev/null
+++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb
@@ -0,0 +1,50 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA
+# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+#
+# Version >= 0.7.15
+# Author: Adam Huffman
+# The Francis Crick Institute
+#
+# Note that upstream development is mainly at: https://github.com/lh3/bwa
+##
+
+name = 'BWA'
+version = '0.7.17'
+
+homepage = 'http://bio-bwa.sourceforge.net/'
+
+description = """
+ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively
+ short nucleotide sequences against a long reference sequence such as the human
+ genome.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/lh3/%(name)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('zlib', '1.2.12'),
+]
+
+# Allow use of x86 intrinsics on PPC
+prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && '
+prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && "
+prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && "
+prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && "
+
+moduleclass = 'bio'

From 5f3a339458779b17acae12408219e79587c34141 Mon Sep 17 00:00:00 2001
From: rocky_build <rocky_build@rocky7.rocky.bio.utk.edu>
Date: Thu, 20 Apr 2023 15:54:41 -0400
Subject: [PATCH 391/601] adding easyconfigs: picard-3.0.0-Java-17.eb

---
 .../p/picard/picard-3.0.0-Java-17.eb          | 60 +++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb

diff --git a/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb b/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb
new file mode 100644
index 00000000000..b9cd29fae76
--- /dev/null
+++ b/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb
@@ -0,0 +1,60 @@
+##
+# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild
+#
+# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia
+# Homepage: https://www.adelaide.edu.au/phoenix/
+#
+# Copyright::   adelaide.edu.au/phoenix
+# Authors::	Robert Qiao <robert.qiao@adelaide.edu.au>, Exe Escobedo <exequiel.sepulvedaescobedo@adelaide.edu.au>
+# License::	MIT
+#
+# 2.10.1:
+# Adam Huffman
+# The Francis Crick Institute
+# 2.18.11:
+# Jonas Demeulemeester
+# The Francis Crick Institute
+# 2.21.1
+# Pavel Grochal (INUITS)
+# 2.25.1
+# J. Sassmannshausen (GSTT)
+# 2.25.5
+# Erica Bianco (HPCNow!)
+# 2.26.10
+# Christoph Siegert (Leipzig University)
+# 3.0.0
+# Graham Derryberry (UTK)
+##
+
+easyblock = 'JAR'
+
+name = 'picard'
+version = '3.0.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://broadinstitute.github.io/picard/'
+description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s']
+sources = [{
+    'filename': '%(name)s-%(version)s.jar',
+    'download_filename': '%(name)s.jar',
+}]
+checksums = ['0d5e28ab301fad3b02030d01923888129ba82c5f722ac5ccb2d418ab76ac5499']
+
+postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"]
+
+dependencies = [('Java', '17')]
+
+sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE']
+
+sanity_check_paths = {
+    'files': ['picard.jar'],
+    'dirs': [],
+}
+
+modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar"
+
+moduleclass = 'bio'

From 41df7683c2463dd409555cb966b31ca132af7b1e Mon Sep 17 00:00:00 2001
From: rocky_build <rocky_build@rocky7.rocky.bio.utk.edu>
Date: Thu, 20 Apr 2023 15:59:22 -0400
Subject: [PATCH 392/601] adding easyconfigs: BEDTools-2.30.0-GCC-12.2.0.eb,
 BamTools-2.5.2-GCC-12.2.0.eb

---
 .../b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb  | 45 +++++++++++++++++++
 .../b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb   | 19 ++++++++
 2 files changed, 64 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb
new file mode 100644
index 00000000000..e85979fa033
--- /dev/null
+++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb
@@ -0,0 +1,45 @@
+# Author: Maxime Schmitt, University of Luxembourg
+# Author: Adam Huffman, The Francis Crick Institute
+#
+# Based on the work of: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics (SIB)
+# Biozentrum - University of Basel
+
+easyblock = 'MakeCp'
+
+name = 'BEDTools'
+version = '2.30.0'
+
+homepage = "https://bedtools.readthedocs.io/"
+description = """BEDTools: a powerful toolset for genome arithmetic.
+The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
+computing coverage.
+The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8']
+
+builddependencies = [('Python', '3.10.8')]
+
+dependencies = [
+    ('XZ', '5.2.7'),
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('BamTools', '2.5.2'),
+]
+
+buildopts = 'CXX="$CXX"'
+
+files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],
+    'dirs': files_to_copy,
+}
+
+sanity_check_commands = ['bedtools --help']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb
new file mode 100644
index 00000000000..324af5c529f
--- /dev/null
+++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb
@@ -0,0 +1,19 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+name = 'BamTools'
+version = '2.5.2'
+
+homepage = 'https://github.com/pezmaster31/bamtools'
+description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files."
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+# https://github.com/pezmaster31/bamtools
+github_account = 'pezmaster31'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8']
+
+builddependencies = [('CMake', '3.24.3')]
+
+moduleclass = 'bio'

From 91b2f308a868a53f24f6fa2576ac588121b7abfa Mon Sep 17 00:00:00 2001
From: rocky_build <rocky_build@rocky7.rocky.bio.utk.edu>
Date: Thu, 20 Apr 2023 16:10:20 -0400
Subject: [PATCH 393/601] adding easyconfigs: VCFtools-0.1.16-GCC-12.2.0.eb

---
 .../v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb  | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb
new file mode 100644
index 00000000000..0ff539325ea
--- /dev/null
+++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'VCFtools'
+version = '0.1.16'
+
+homepage = "https://vcftools.github.io"
+description = """The aim of VCFtools is to provide 
+ easily accessible methods for working with complex 
+ genetic variation data in the form of VCF files."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3']
+
+builddependencies = [
+    ('pkgconf', '1.9.3'),
+]
+
+dependencies = [
+    ('Perl', '5.36.0'),
+    ('HTSlib', '1.17'),
+    ('zlib', '1.2.12'),
+]
+
+modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'}
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

From 419dd75458e298d013b5f5e34a44fe27fdeff718 Mon Sep 17 00:00:00 2001
From: rocky_build <rocky_build@rocky7.rocky.bio.utk.edu>
Date: Thu, 20 Apr 2023 17:10:57 -0400
Subject: [PATCH 394/601] adding easyconfigs: Trimmomatic-0.39-Java-17.eb

---
 .../t/Trimmomatic/Trimmomatic-0.39-Java-17.eb | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb

diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb
new file mode 100644
index 00000000000..5f9d39b5c69
--- /dev/null
+++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb
@@ -0,0 +1,32 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+
+easyblock = 'Tarball'
+
+name = 'Trimmomatic'
+version = '0.39'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://www.usadellab.org/cms/?page=trimmomatic'
+description = """Trimmomatic performs a variety of useful trimming tasks for illumina 
+ paired-end and single ended data.The selection of trimming steps and their associated 
+ parameters are supplied on the command line. """
+
+toolchain = SYSTEM
+
+source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/']
+sources = [SOURCE_ZIP]
+checksums = ['2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca']
+
+dependencies = [('Java', '17')]
+
+modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n"""
+
+sanity_check_paths = {
+    'files': ["trimmomatic-%(version)s.jar"],
+    'dirs': [""],
+}
+
+moduleclass = 'bio'

From 93b611fb04dc319f31a1bb9e483a0d62ee9fe6ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 21 Apr 2023 00:18:53 +0200
Subject: [PATCH 395/601] Version bump Java to latest builds that include ppc

---
 easybuild/easyconfigs/j/Java/Java-11.0.18.eb | 30 +++++++++++++++++++
 easybuild/easyconfigs/j/Java/Java-11.eb      |  2 +-
 easybuild/easyconfigs/j/Java/Java-17.0.6.eb  | 30 +++++++++++++++++++
 easybuild/easyconfigs/j/Java/Java-17.eb      |  2 +-
 easybuild/easyconfigs/j/Java/Java-8.362.eb   | 31 ++++++++++++++++++++
 easybuild/easyconfigs/j/Java/Java-8.eb       |  2 +-
 6 files changed, 94 insertions(+), 3 deletions(-)
 create mode 100644 easybuild/easyconfigs/j/Java/Java-11.0.18.eb
 create mode 100644 easybuild/easyconfigs/j/Java/Java-17.0.6.eb
 create mode 100644 easybuild/easyconfigs/j/Java/Java-8.362.eb

diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.18.eb b/easybuild/easyconfigs/j/Java/Java-11.0.18.eb
new file mode 100644
index 00000000000..c41c7c582f9
--- /dev/null
+++ b/easybuild/easyconfigs/j/Java/Java-11.0.18.eb
@@ -0,0 +1,30 @@
+name = 'Java'
+version = '11.0.18'
+local_build = '10'
+
+homepage = 'http://openjdk.java.net'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+Java applications on desktops and servers."""
+
+toolchain = SYSTEM
+
+local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz'
+
+# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions
+
+source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/'
+               % local_build]
+sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)]
+
+checksums = [
+    {
+        local_tarball_tmpl % ('x64', local_build):
+            '4a29efda1d702b8ff38e554cf932051f40ec70006caed5c4857a8cbc7a0b7db7',
+        local_tarball_tmpl % ('aarch64', local_build):
+            '04d5eeff6a6449bcdca0f52cd97bafd43ce09d40ef1e73fa0e1add63bea4a9c8',
+        local_tarball_tmpl % ('ppc64le', local_build):
+            '459148d489b08ceec2d901e950ac36722b4c55e907e979291ddfc954ebdcea47',
+    }
+]
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb
index d53c0b9b2f5..77086a3e1b8 100644
--- a/easybuild/easyconfigs/j/Java/Java-11.eb
+++ b/easybuild/easyconfigs/j/Java/Java-11.eb
@@ -9,6 +9,6 @@ Java applications on desktops and servers."""
 
 toolchain = SYSTEM
 
-dependencies = [('Java', '%(version)s.0.16')]
+dependencies = [('Java', '%(version)s.0.18')]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.6.eb b/easybuild/easyconfigs/j/Java/Java-17.0.6.eb
new file mode 100644
index 00000000000..71d89858ea4
--- /dev/null
+++ b/easybuild/easyconfigs/j/Java/Java-17.0.6.eb
@@ -0,0 +1,30 @@
+name = 'Java'
+version = '17.0.6'
+local_build = '10'
+
+homepage = 'http://openjdk.java.net'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+Java applications on desktops and servers."""
+
+toolchain = SYSTEM
+
+local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz'
+
+# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions
+
+source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/'
+               % local_build]
+sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)]
+
+checksums = [
+    {
+        local_tarball_tmpl % ('x64', local_build):
+            'a0b1b9dd809d51a438f5fa08918f9aca7b2135721097f0858cf29f77a35d4289',
+        local_tarball_tmpl % ('aarch64', local_build):
+            '9e0e88bbd9fa662567d0c1e22d469268c68ac078e9e5fe5a7244f56fec71f55f',
+        local_tarball_tmpl % ('ppc64le', local_build):
+            'cb772c3fdf3f9fed56f23a37472acf2b80de20a7113fe09933891c6ef0ecde95',
+    }
+]
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Java/Java-17.eb b/easybuild/easyconfigs/j/Java/Java-17.eb
index b5936b5a154..1efea31e843 100644
--- a/easybuild/easyconfigs/j/Java/Java-17.eb
+++ b/easybuild/easyconfigs/j/Java/Java-17.eb
@@ -9,6 +9,6 @@ Java applications on desktops and servers."""
 
 toolchain = SYSTEM
 
-dependencies = [('Java', '%(version)s.0.4')]
+dependencies = [('Java', '%(version)s.0.6')]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Java/Java-8.362.eb b/easybuild/easyconfigs/j/Java/Java-8.362.eb
new file mode 100644
index 00000000000..f8c6b809aa0
--- /dev/null
+++ b/easybuild/easyconfigs/j/Java/Java-8.362.eb
@@ -0,0 +1,31 @@
+name = 'Java'
+version = '8.362'
+local_build = 'b09'
+
+homepage = 'http://openjdk.java.net'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+Java applications on desktops and servers."""
+
+toolchain = SYSTEM
+
+local_tarball_tmpl = 'OpenJDK8U-jdk_%s_linux_hotspot_%%(version_major)su%%(version_minor)s%s.tar.gz'
+
+# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions
+
+source_urls = ['https://github.com/adoptium/temurin8-binaries/releases/download/'
+               'jdk%%(version_major)su%%(version_minor)s-%s/' % local_build]
+sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)]
+
+checksums = [
+    {
+        local_tarball_tmpl % ('x64', local_build):
+            '1486a792fb224611ce0cd0e83d4aacd3503b56698549f8e9a9f0a6ebb83bdba1',
+        local_tarball_tmpl % ('aarch64', local_build):
+            '9290a8beefd7a94f0eb030f62d402411a852100482b9c5b63714bacc57002c2a',
+        local_tarball_tmpl % ('ppc64le', local_build):
+            '69658dd316c6a160915655971573179766e19c6610ea03880c1e578a0e518f74',
+
+    }
+]
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/j/Java/Java-8.eb b/easybuild/easyconfigs/j/Java/Java-8.eb
index 8c9091f83dd..854eccb56cb 100644
--- a/easybuild/easyconfigs/j/Java/Java-8.eb
+++ b/easybuild/easyconfigs/j/Java/Java-8.eb
@@ -9,6 +9,6 @@ Java applications on desktops and servers."""
 
 toolchain = SYSTEM
 
-dependencies = [('Java', '%(version)s.345')]
+dependencies = [('Java', '%(version)s.362')]
 
 moduleclass = 'lang'

From 5ab3f23585ade0e16822ce16fc09c01d5a565c21 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 21 Apr 2023 13:45:14 +0200
Subject: [PATCH 396/601] adding easyconfigs:
 pod5-file-format-0.1.8-foss-2022a.eb and patches:
 pod5-file-format-0.1.8_dep_fix.patch

---
 .../pod5-file-format-0.1.8-foss-2022a.eb      | 81 +++++++++++++++++++
 .../pod5-file-format-0.1.8_dep_fix.patch      | 22 +++++
 2 files changed, 103 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch

diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
new file mode 100644
index 00000000000..b924d3aef43
--- /dev/null
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
@@ -0,0 +1,81 @@
+easyblock = 'CMakeMake'
+
+name = 'pod5-file-format'
+version = '0.1.8'
+
+homepage = 'https://github.com/nanoporetech/pod5-file-format'
+description = """POD5 is a file format for storing nanopore dna data in an easily accessible way.
+ The format is able to be written in a streaming manner which allows a sequencing
+ instrument to directly write the format."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/nanoporetech/%(name)s/archive/']
+sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+patches = ['pod5-file-format-0.1.8_dep_fix.patch']
+checksums = [
+    {'pod5-file-format-0.1.8.tar.gz': '262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'},
+    {'pod5-file-format-0.1.8_dep_fix.patch': 'd05e52467387c67bc87551eccbf5a6c3253ad1c4019eaf21ad861895e9a086c6'},
+]
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Arrow', '8.0.0'),
+    ('SciPy-bundle', '2022.05'),
+    ('zstd', '1.5.2'),
+    ('flatbuffers', '2.0.0'),
+    ('pybind11', '2.9.2'),
+    ('Boost', '1.79.0'),
+    ('build', '0.10.0'),
+    ('pkg-config', '0.29.2'),
+    ('HDF5', '1.12.2'),
+    ('h5py', '3.7.0'),
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'download_dep_fail': True,
+    'use_pip': True,
+    'sanity_pip_check': True,
+    'installopts': '',
+}
+
+exts_list = [
+    ('pkgconfig', '1.5.5', {
+        'checksums': ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'],
+    }),
+    ('attrs', '22.2.0', {
+        'checksums': ['c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99'],
+    }),
+    ('vbz_h5py_plugin', '1.0.1', {
+        'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'],
+    }),
+    ('iso8601', '1.1.0', {
+        'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'],
+    }),
+    ('pod5', version, {
+        'source_urls': source_urls,
+        'sources': sources,
+        'start_dir': 'python/pod5',
+        'checksums': ['262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'],
+    }),
+]
+
+configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib/libzstd.a" '
+
+installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s'
+installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl'
+
+postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl']
+
+sanity_check_commands = ['pod5 subset --help']
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
new file mode 100644
index 00000000000..2782bdeb102
--- /dev/null
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
@@ -0,0 +1,22 @@
+diff -u pod5-file-format-0.1.8/c++/CMakeLists.txt.orig pod5-file-format-0.1.8/c++/CMakeLists.txt
+--- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig	2023-01-20 12:22:05.000000000 +0100
++++ pod5-file-format-0.1.8/c++/CMakeLists.txt	2023-01-23 10:11:12.097686513 +0100
+@@ -21,6 +21,7 @@
+ endif()
+ 
+ find_package(Threads REQUIRED)
++find_package(pybind11 REQUIRED)
+ 
+ find_program(
+     FLATBUFFERS_FLATC_EXECUTABLE
+diff -u pod5-file-format-0.1.8/CMakeLists.txt.orig pod5-file-format-0.1.8/CMakeLists.txt
+--- pod5-file-format-0.1.8/CMakeLists.txt.orig	2023-01-20 12:22:05.000000000 +0100
++++ pod5-file-format-0.1.8/CMakeLists.txt	2023-01-23 10:34:44.860294168 +0100
+@@ -92,7 +91,6 @@
+
+ if (BUILD_PYTHON_WHEEL)
+     find_package (Python ${PYTHON_VERSION} EXACT COMPONENTS Interpreter Development)
+-    add_subdirectory(third_party/pybind11)
+ endif()
+
+ add_subdirectory(c++)

From 7094086458de57a7c32002f30a61021a0ac29d72 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 21 Apr 2023 13:49:55 +0200
Subject: [PATCH 397/601] add missing dependency

---
 .../build-0.10.0-foss-2022a.eb                | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb
new file mode 100644
index 00000000000..ce8f9a50a22
--- /dev/null
+++ b/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'build'
+version = '0.10.0'
+
+homepage = 'https://github.com/pypa/build'
+description = """A simple, correct Python build frontend."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pyparsing', '3.0.9', {
+        'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'],
+    }),
+    ('packaging', '20.4', {
+        'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'],
+    }),
+    ('tomli', '2.0.1', {
+        'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'],
+    }),
+    ('pyproject_hooks', '1.0.0', {
+        'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'],
+    }),
+    (name, version, {
+        'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'],
+    }),
+]
+
+sanity_check_commands = [
+    "python3 -m build -V",
+]
+
+moduleclass = 'devel'

From 71b1f09fb6ac48e3be5e92ba92cdb1e7bd4c1b7c Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Fri, 21 Apr 2023 14:00:35 +0200
Subject: [PATCH 398/601] adding easyconfigs: OptaDOS-1.2.380-GCC-11.3.0.eb

---
 .../o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb   | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb
new file mode 100644
index 00000000000..99a1e6a6a88
--- /dev/null
+++ b/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'MakeCp'
+
+name = 'OptaDOS'
+version = '1.2.380'
+
+homepage = 'http://www.optados.org/'
+description = """OptaDOS is a program for calculating core-electron and low-loss electron energy
+loss spectra (EELS) and optical spectra along with total-, projected- and
+joint-density of electronic states (DOS) from single-particle eigenenergies and
+dipole transition coefficients."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'optados-developers'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['606d3db28dba791f62b05ef638ed0b1e42474763db65e04abd63a30501bb2eac']
+
+buildopts = "SYSTEM=gfortran COMMS_ARCH=serial PREFIX=%(installdir)s "
+buildopts += 'FFLAGS="$FFLAGS -fconvert=big-endian -ffree-line-length-150"'
+
+files_to_copy = [
+    (['src/%(namelower)s.gfortran.*'], 'bin'),
+    'documents',
+    'examples',
+    'tools',
+]
+
+postinstallcmds = [
+    "cd %(installdir)s/bin && ln -s %(namelower)s.gfortran.* %(namelower)s",
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['documents', 'examples', 'tools']
+}
+
+sanity_check_commands = ['%(namelower)s --help']
+
+moduleclass = 'phys'

From 96f79baf307404cdeb0c1041d5be7119875876ea Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 21 Apr 2023 14:31:00 +0200
Subject: [PATCH 399/601] add sanity check paths

---
 .../p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb  | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
index b924d3aef43..15436f8c712 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
@@ -74,6 +74,11 @@ installopts += ' && pip install --no-deps --ignore-installed --prefix %(installd
 
 postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl']
 
+sanity_check_paths = {
+    'files': ['bin/pod5', 'lib/libpod5_format.a'],
+    'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'],
+}
+
 sanity_check_commands = ['pod5 subset --help']
 
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}

From fbd9fa617cd0291cca3baa2476f608bd82efa189 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 21 Apr 2023 15:22:44 +0200
Subject: [PATCH 400/601] Add egg file to OpenCV 4.6.0 python package for pip

---
 .../OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 8 ++++++++
 .../o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb           | 8 ++++++++
 .../easyconfigs/o/OpenCV/opencv-contrib-python.egg-info   | 5 +++++
 3 files changed, 21 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info

diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
index 70276c87526..2e67ca665c5 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
@@ -32,6 +32,7 @@ sources = [
         'extract_cmd': 'cp %s %(builddir)s'
     },
 ]
+patches = [('opencv-contrib-python.egg-info', '..')]
 checksums = [
     '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359',  # opencv-4.6.0.zip
     '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3',  # opencv_contrib-4.6.0.zip
@@ -82,6 +83,13 @@ configopts = " ".join([
     "-DCUDA_NVCC_FLAGS=--std=c++14",
 ])
 
+# Install a egg-info file so it is more python friendly
+local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info'
+postinstallcmds = [
+    'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
+]
+
 enhance_sanity_check = True
 
 local_contrib_libs = [
diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
index b957c01b7d4..c764ad56a61 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
@@ -31,6 +31,7 @@ sources = [
         'extract_cmd': 'cp %s %(builddir)s'
     },
 ]
+patches = [('opencv-contrib-python.egg-info', '..')]
 checksums = [
     '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359',  # opencv-4.6.0.zip
     '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3',  # opencv_contrib-4.6.0.zip
@@ -78,6 +79,13 @@ configopts = " ".join([
     "-DBUILD_opencv_python2=OFF",
 ])
 
+# Install a egg-info file so it is more python friendly
+local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info'
+postinstallcmds = [
+    'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
+]
+
 enhance_sanity_check = True
 
 local_contrib_libs = [
diff --git a/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info b/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info
new file mode 100644
index 00000000000..073e127f34d
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info
@@ -0,0 +1,5 @@
+Metadata-Version: 2.1
+Name: opencv-contrib-python
+Version: #OPENCV_VERSION#
+Summary: Wrapper package for OpenCV python bindings.
+Platform: UNKNOWN

From 88bd6ba8e0092fce9c63b0ec5a0450bc361b8e07 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 21 Apr 2023 15:24:09 +0200
Subject: [PATCH 401/601] adding easyconfigs: RepeatMasker-4.1.5-foss-2022a.eb

---
 .../RepeatMasker-4.1.5-foss-2022a.eb          | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb

diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb
new file mode 100644
index 00000000000..d7e8df4c81d
--- /dev/null
+++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb
@@ -0,0 +1,57 @@
+easyblock = 'Tarball'
+
+name = 'RepeatMasker'
+version = '4.1.5'
+
+homepage = 'https://www.repeatmasker.org/'
+description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats
+ and low complexity DNA sequences."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://www.repeatmasker.org/%(name)s']
+sources = [
+    SOURCE_TAR_GZ,
+    # optional but recommended: RepBase RepeatMasker Edition
+    # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php
+    # {
+    #     'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz',
+    #     'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1",
+    # },
+]
+checksums = ['16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('Perl', '5.34.1'),
+    ('TRF', '4.09.1'),
+    ('h5py', '3.7.0'),
+    # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match
+    ('HMMER', '3.3.2'),
+    ('RMBlast', '2.13.0'),
+]
+
+local_default_search_engine = 'RMBlast'
+
+local_config_command = 'cd %(installdir)s &&'
+local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" '
+local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" '
+local_config_command += '-default_search_engine %s' % local_default_search_engine.lower()
+
+postinstallcmds = [local_config_command]
+
+fix_perl_shebang_for = ['RepeatMasker']
+
+sanity_check_paths = {
+    'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'],
+    'dirs': ['Libraries', 'util'],
+}
+
+sanity_check_commands = ['RepeatMasker -help']
+
+modextrapaths = {
+    'PATH': '',
+    'PERL5LIB': '',
+}
+
+moduleclass = 'bio'

From e04695b0a53f6d4fd861e0aacbe37b6e8714ae8b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 21 Apr 2023 16:34:11 +0200
Subject: [PATCH 402/601] Fix checksums

---
 .../OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 8 +++++---
 .../o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb           | 8 +++++---
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
index 2e67ca665c5..0edcf1239a6 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
@@ -34,9 +34,11 @@ sources = [
 ]
 patches = [('opencv-contrib-python.egg-info', '..')]
 checksums = [
-    '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359',  # opencv-4.6.0.zip
-    '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3',  # opencv_contrib-4.6.0.zip
-    '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246',  # ippicv_2020_lnx_intel64_20191018_general.tgz
+    {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'},
+    {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'},
+    {'ippicv_2020_lnx_intel64_20191018_general.tgz':
+     '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'},
+    {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'},
 ]
 
 builddependencies = [
diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
index c764ad56a61..6373a8db53e 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
@@ -33,9 +33,11 @@ sources = [
 ]
 patches = [('opencv-contrib-python.egg-info', '..')]
 checksums = [
-    '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359',  # opencv-4.6.0.zip
-    '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3',  # opencv_contrib-4.6.0.zip
-    '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246',  # ippicv_2020_lnx_intel64_20191018_general.tgz
+    {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'},
+    {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'},
+    {'ippicv_2020_lnx_intel64_20191018_general.tgz':
+     '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'},
+    {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'},
 ]
 
 builddependencies = [

From d25f27151ae72d8e102221218158f36427da4c56 Mon Sep 17 00:00:00 2001
From: sam <sammoors@gmail.com>
Date: Fri, 21 Apr 2023 17:01:34 +0200
Subject: [PATCH 403/601] adding easyconfigs: ReaxFF-2.0-GCC-11.3.0.eb

---
 .../r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb         | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb
new file mode 100644
index 00000000000..a3082257b1f
--- /dev/null
+++ b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'MakeCp'
+
+name = 'ReaxFF'
+version = '2.0'
+
+homepage = 'https://www.engr.psu.edu/adri/ReaxffManual.aspx'
+
+description = """
+REAXFF Reactive force field program
+"""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['a62829d25b6eb5c311206a89a892e1de6fd3ee33cae40489901bb9f50d53f4d2']
+
+download_instructions = """
+Register at https://www.engr.psu.edu/adri/Home.aspx and follow instructions
+"""
+
+buildopts = 'SUFFIX="-c -O3 -std=legacy"'
+
+files_to_copy = [
+    (['reac'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/reac'],
+    'dirs': [],
+}
+
+moduleclass = 'chem'

From 2c713d31877460663643e3298a5ee98238540ff0 Mon Sep 17 00:00:00 2001
From: Arnold Kole <35299166+ahkole@users.noreply.github.com>
Date: Sat, 22 Apr 2023 01:14:01 +0200
Subject: [PATCH 404/601] Remove explicit setting of default option

---
 easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb
index 6dba042d193..3b6c72c06b5 100644
--- a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb
@@ -20,8 +20,6 @@ builddependencies = [
     ('CMake', '3.23.1'),
 ]
 
-separate_build_dir = True
-
 sanity_check_paths = {
     'files': ['lib/libpsml.a'],
     'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libpsml'],

From f324ff1f8ea8f06067e5ee00bb009dbd577acd82 Mon Sep 17 00:00:00 2001
From: Arnold Kole <35299166+ahkole@users.noreply.github.com>
Date: Sat, 22 Apr 2023 01:15:24 +0200
Subject: [PATCH 405/601] Restrict to serial compilation to fix build error

---
 .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb      | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
index 1b2f864e5f2..7373a16da20 100644
--- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
+++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
@@ -22,6 +22,8 @@ builddependencies = [
     ('CMake', '3.23.1'),
 ]
 
+parallel = 1
+
 sanity_check_paths = {
     'files': ['lib/libgridxc.a'],
     'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'],

From a228a0c137b93ef5b2eaef61481a2e52988cb3ef Mon Sep 17 00:00:00 2001
From: Arnold Kole <35299166+ahkole@users.noreply.github.com>
Date: Sat, 22 Apr 2023 12:31:39 +0200
Subject: [PATCH 406/601] Fixed failed build to the pkg-config dependency

---
 .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb     | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
index 7373a16da20..474990ff216 100644
--- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
+++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
@@ -16,10 +16,13 @@ checksums = ['e7883e57a4db2438ee59437740291c06e0cfe1c8ae1901e4001f32312307e46a']
 
 configopts = "-DWITH_MPI=ON -DWITH_LIBXC=ON"
 
+preconfigopts = 'CPATH= '  # gfortran ignores CPATH, but pkgconf also excludes dirs from CPATH
+
 dependencies = [('libxc', '5.2.3')]
 
 builddependencies = [
     ('CMake', '3.23.1'),
+    ('pkgconf', '1.8.0'),
 ]
 
 parallel = 1

From a0086d5881e7c7bbd7e7c7999638fb3f59a68933 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Sat, 22 Apr 2023 22:42:31 +0200
Subject: [PATCH 407/601] adding easyconfigs:
 CLIP-20230220-foss-2022a-CUDA-11.7.0.eb

---
 .../CLIP-20230220-foss-2022a-CUDA-11.7.0.eb   | 41 +++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..cacf9b91d85
--- /dev/null
+++ b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'CLIP'
+version = '20230220'
+versionsuffix = '-CUDA-%(cudaver)s'
+_commit = 'a9b1bf5'
+
+homepage = 'https://github.com/openai/CLIP'
+description = """
+CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a
+variety of (image, text) pairs. It can be instructed in natural language to
+predict the most relevant text snippet, given an image, without directly
+optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and
+3."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('PyTorch', '1.12.0', versionsuffix),
+    ('tqdm', '4.64.0'),
+    ('torchvision', '0.13.1', versionsuffix),
+]
+
+use_pip = True
+
+exts_list = [
+    ('ftfy', '6.1.1', {
+        'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/openai/CLIP/archive'],
+        'sources': [{'download_filename': 'a9b1bf5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'checksums': ['9cbe833d1a8c1d5ea6db87c290119fda4d35a3fe2f7a94d6a88779de502a98e3'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lib'

From 774535448b8662609c69af7e8e8ebc118577d8be Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Sun, 23 Apr 2023 12:51:41 +0200
Subject: [PATCH 408/601] adding easyconfigs: Meep-1.26.0-foss-2020b.eb,
 Guile-3.0.9-GCCcore-10.2.0.eb, libGDSII-0.21-GCCcore-10.2.0.eb,
 libctl-4.5.1-GCCcore-10.2.0.eb, Harminv-1.4.2-foss-2020b.eb,
 MPB-1.11.1-foss-2020b.eb

---
 .../g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb     | 46 ++++++++++++++++
 .../h/Harminv/Harminv-1.4.2-foss-2020b.eb     | 28 ++++++++++
 .../libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb  | 26 +++++++++
 .../l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb   | 31 +++++++++++
 .../m/MPB/MPB-1.11.1-foss-2020b.eb            | 48 +++++++++++++++++
 .../m/Meep/Meep-1.26.0-foss-2020b.eb          | 53 +++++++++++++++++++
 6 files changed, 232 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb
 create mode 100644 easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb
 create mode 100644 easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb
 create mode 100644 easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb
 create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb

diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..cd161186dfc
--- /dev/null
+++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb
@@ -0,0 +1,46 @@
+easyblock = 'ConfigureMake'
+
+name = 'Guile'
+version = '3.0.9'
+
+homepage = 'https://www.gnu.org/software/guile/'
+
+description = """
+ Guile is a programming language, designed to help programmers create flexible
+ applications that can be extended by users or other programmers with plug-ins,
+ modules, or scripts.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['18525079ad29a0d46d15c76581b5d91c8702301bfd821666d2e1d13726162811']
+
+builddependencies = [
+    ('Autotools', '20200321'),
+    ('binutils', '2.35'),
+    ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+    ('gc', '8.2.2'),
+    ('GMP', '6.2.0'),
+    ('libffi', '3.3'),
+    ('libunistring', '1.1'),
+]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"]
+
+sanity_check_paths = {
+    'files': ['bin/guild', 'bin/guile', 'bin/guile-config',
+              'bin/guile-snarf', 'bin/guile-tools',
+              'include/guile/%(version_major_minor)s/libguile.h',
+              'lib/libguile-%(version_major_minor)s.a',
+              'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT],
+    'dirs': ['include/guile/%(version_major_minor)s/libguile',
+             'lib/guile/%(version_major_minor)s/ccache'],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb
new file mode 100644
index 00000000000..7065f827a27
--- /dev/null
+++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'Harminv'
+version = '1.4.2'
+
+homepage = 'https://github.com/stevengj/harminv'
+description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion -
+ given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially
+ decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those
+ sinusoids."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'}
+
+source_urls = ['https://github.com/stevengj/harminv/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5a9a1bf710972442f065d0d62c62d0c4ec3da4a3696d7160a35602c9470bc7a2']
+
+builddependencies = [('pkg-config', '0.29.2')]
+
+configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared"
+
+sanity_check_paths = {
+    'files': ['bin/harminv', 'lib/libharminv.a', 'lib/libharminv.%s' % SHLIB_EXT],
+    'dirs': ['include']
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..5ebb3d807a4
--- /dev/null
+++ b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'libGDSII'
+version = '0.21'
+
+homepage = 'https://github.com/HomerReid/libGDSII'
+description = """libGDSII is a C++ library for working with GDSII binary data files,
+ intended primarily for use with the computational electromagnetism codes
+ scuff-em and meep but sufficiently general-purpose to allow other uses as well."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ['https://github.com/HomerReid/libGDSII/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['31c90a4fb699746d051c0c597ef0543889c9f17b2a711fed398756ac4f1b1f4c']
+
+builddependencies = [
+    ('binutils', '2.35'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/GDSIIConvert', 'include/libGDSII.h', 'lib/libGDSII.a', 'lib/libGDSII.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..3dfc9fe295b
--- /dev/null
+++ b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'libctl'
+version = '4.5.1'
+
+homepage = 'https://libctl.readthedocs.io/en/latest/'
+description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/NanoComp/libctl/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['fcfeb2f13dda05b560f0ec6872757d9318fdfe8f4bc587eb2053a29ba328ae25']
+
+builddependencies = [
+    ('binutils', '2.35'),
+    ('Autotools', '20200321'),  # required for libtool
+]
+
+dependencies = [('Guile', '3.0.9')]
+
+configopts = '--with-pic --enable-shared'
+
+sanity_check_paths = {
+    'files': ['bin/gen-ctl-io', 'lib/libctl.a', 'lib/libctlgeom.a',
+              'lib/libctlgeom.%s' % SHLIB_EXT, 'lib/libctl.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb
new file mode 100644
index 00000000000..bff6686a320
--- /dev/null
+++ b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb
@@ -0,0 +1,48 @@
+easyblock = 'ConfigureMake'
+
+name = 'MPB'
+version = '1.11.1'
+
+homepage = 'https://mpb.readthedocs.io/en/latest/'
+description = """MPB is a free and open-source software package for computing
+ the band structures, or dispersion relations, and electromagnetic
+ modes of periodic dielectric structures, on both serial
+ and parallel computers. MPB is an acronym for MIT Photonic Bands."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://github.com/NanoComp/mpb/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['dc55b081c56079727dac92d309f8e4ea84ca6eea9122ec24b7955f8c258608e1']
+
+builddependencies = [
+    ('Autotools', '20200321'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('HDF5', '1.10.7'),
+    ('libctl', '4.5.1'),
+    ('Guile', '3.0.9'),
+    ('libreadline', '8.0'),
+]
+
+local_common_configopts = "--with-pic --with-blas=openblas --with-lapack=openblas "
+local_common_configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared "
+
+configopts = [
+    local_common_configopts + " ",
+    local_common_configopts + " --with-inv-symmetry",
+    local_common_configopts + " --with-mpi ",
+    local_common_configopts + " --with-mpi --with-inv-symmetry",
+]
+
+sanity_check_paths = {
+    'files': ['bin/mpb%s' % x for x in ['', '-data', 'i', 'i-data', 'i-mpi', 'i-split', '-mpi', '-split']] +
+             ['lib/libmpb.a', 'lib/libmpbi_mpi.a', 'lib/libmpbi.a', 'lib/libmpb_mpi.a', 'lib/libmpb.%s' % SHLIB_EXT,
+              'lib/libmpbi_mpi.%s' % SHLIB_EXT, 'lib/libmpbi.%s' % SHLIB_EXT, 'lib/libmpb_mpi.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'phys'
diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb
new file mode 100644
index 00000000000..d7c07a5167e
--- /dev/null
+++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb
@@ -0,0 +1,53 @@
+easyblock = 'ConfigureMake'
+
+name = 'Meep'
+version = '1.26.0'
+
+homepage = 'https://meep.readthedocs.io/en/latest/'
+description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package
+ developed at MIT to model electromagnetic systems."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+toolchainopts = {'usempi': True, 'opt': True, 'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/NanoComp/meep/releases/download/v%(version)s/']
+sources = ['meep-%(version)s.tar.gz']
+checksums = ['3f89f1bd781e46b938aa02e315a4526a4ae9896687db75c187b4f17febcbc301']
+
+builddependencies = [
+    ('Autotools', '20200321'),
+    ('pkg-config', '0.29.2'),
+    ('SWIG', '4.0.2')
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('matplotlib', '3.3.3'),
+    ('MPB', '1.11.1'),
+    ('Harminv', '1.4.2'),
+    ('HDF5', '1.10.7'),
+    ('libctl', '4.5.1'),
+    ('libGDSII', '0.21'),
+    ('GSL', '2.6'),
+    ('Guile', '3.0.9'),
+]
+
+configopts = "--with-pic --with-mpi --with-blas=openblas --with-lapack=openblas --without-gcc-arch "
+configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared "
+configopts += "LDFLAGS=$LDFLAGS+' -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lmpi_mpifh'"
+
+sanity_check_paths = {
+    'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libpympb.a',
+              'lib/libmeep.%s' % SHLIB_EXT, 'lib/libpympb.%s' % SHLIB_EXT],
+    'dirs': ['include/meep', 'lib/python%(pyshortver)s/site-packages/meep', 'share/meep'],
+}
+
+sanity_check_commands = [
+    "meep --help",
+    "python -c 'import meep'",
+]
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'phys'

From 5c8b0fef7eab2f9bd10d6f6bdaf1f646f4503339 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 24 Apr 2023 01:46:43 +0200
Subject: [PATCH 409/601] adding easyconfigs: SOCI-4.0.3-GCC-12.2.0.eb

---
 .../s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb           | 52 +++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb

diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb
new file mode 100644
index 00000000000..2b1ee760c82
--- /dev/null
+++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb
@@ -0,0 +1,52 @@
+easyblock = 'CMakeMake'
+
+name = 'SOCI'
+version = '4.0.3'
+
+homepage = 'http://soci.sourceforge.net/'
+description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the
+ regular C++ code, staying entirely within the Standard C++."""
+
+toolchain = {'name': 'GCC', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/SOCI/soci/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928']
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+]
+
+dependencies = [
+    ('Boost', '1.81.0'),
+    ('SQLite', '3.39.4'),
+    ('PostgreSQL', '15.2'),
+]
+
+# Matches RStudio (1.4.1717) install options
+# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci
+configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true "
+configopts += "-DSOCI_TESTS=OFF "
+configopts += "-DSOCI_CXX11=ON "
+configopts += "-DSOCI_EMPTY=OFF "
+configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" '
+configopts += "-DBoost_USE_STATIC_LIBS=ON "
+configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" '
+configopts += "-DWITH_BOOST=ON "
+configopts += "-DWITH_POSTGRESQL=ON "
+configopts += "-DWITH_SQLITE3=ON "
+configopts += "-DWITH_DB2=OFF "
+configopts += "-DWITH_MYSQL=OFF "
+configopts += "-DWITH_ORACLE=OFF "
+configopts += "-DWITH_FIREBIRD=OFF "
+configopts += "-DWITH_ODBC=OFF "
+configopts += "-DBoost_DEBUG=1 "
+
+local_dbs = ['postgresql', 'sqlite3']
+
+sanity_check_paths = {
+    'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']],
+    'dirs': ['include/soci/%s' % x for x in local_dbs],
+}
+
+moduleclass = 'lang'

From 237961a9f21e32ce3c15f9f8bb1034e2877d239a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 24 Apr 2023 02:24:44 +0200
Subject: [PATCH 410/601] adding easyconfigs: yaml-cpp-0.7.0-GCCcore-12.2.0.eb

---
 .../yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..e09fb068964
--- /dev/null
+++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb
@@ -0,0 +1,30 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = 'CMakeMake'
+name = 'yaml-cpp'
+version = '0.7.0'
+
+homepage = "https://github.com/jbeder/yaml-cpp"
+description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/jbeder/%(name)s/archive/']
+sources = ['%(name)s-%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_fix-cmake-export.patch']
+checksums = [
+    '43e6a9fcb146ad871515f0d0873947e5d497a1c9c60c58cb102a97b47208b7c3',
+    'c562a575bbb161af478795e43bfd9073e3f874bea07134a321c1063cd7098c1c',  # yaml-cpp-0.7.0_fix-cmake-export.patch
+]
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3')
+]
+
+sanity_check_paths = {
+    'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'],
+    'dirs': ['lib', 'include'],
+}
+
+moduleclass = 'tools'

From 82b53e7248db4480428658ea85f9b8074e66295e Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Mon, 24 Apr 2023 10:10:10 +0200
Subject: [PATCH 411/601] use commit var

---
 .../easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb
index cacf9b91d85..e7b38dfeff1 100644
--- a/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb
@@ -31,7 +31,7 @@ exts_list = [
     }),
     (name, version, {
         'source_urls': ['https://github.com/openai/CLIP/archive'],
-        'sources': [{'download_filename': 'a9b1bf5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
+        'sources': [{'download_filename': _commit + '.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}],
         'checksums': ['9cbe833d1a8c1d5ea6db87c290119fda4d35a3fe2f7a94d6a88779de502a98e3'],
     }),
 ]

From 036204609a0617c9df77ab705e352db5d717fa44 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Mon, 24 Apr 2023 11:42:29 +0200
Subject: [PATCH 412/601] gc v8.0.4, libunistring v1.1 and update to Meep
 v1.26.0

---
 .../g/gc/gc-8.2.2-GCCcore-10.2.0.eb           | 42 +++++++++++++++++++
 .../libunistring-1.1-GCCcore-10.2.0.eb        | 31 ++++++++++++++
 .../m/Meep/Meep-1.26.0-foss-2020b.eb          |  1 -
 3 files changed, 73 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb
 create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb

diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..5061399f2ff
--- /dev/null
+++ b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'ConfigureMake'
+
+name = 'gc'
+version = '8.2.2'
+local_libatomic_version = '7.8.0'
+
+homepage = 'https://hboehm.info/gc/'
+description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a
+ garbage collecting replacement for C malloc or C++ new.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = [
+    'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/',  # preferred for gc-%(version)s.tar.gz
+    'https://hboehm.info/gc/gc_source/',  # alternate for gc-%(version)s.tar.gz
+    'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version,
+]
+sources = [
+    SOURCE_TAR_GZ,
+    'libatomic_ops-%s.tar.gz' % local_libatomic_version,
+]
+checksums = [
+    {'gc-8.2.2.tar.gz': 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0'},
+    {'libatomic_ops-7.8.0.tar.gz': '15676e7674e11bda5a7e50a73f4d9e7d60452271b8acf6fd39a71fefdf89fa31'},
+]
+
+builddependencies = [
+    ('binutils', '2.35'),
+]
+
+preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && '
+
+configopts = "--enable-static"
+
+sanity_check_paths = {
+    'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT,
+              'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT],
+    'dirs': ['include/gc', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..f93fd922791
--- /dev/null
+++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'libunistring'
+version = '1.1'
+
+homepage = 'https://www.gnu.org/software/libunistring/'
+
+description = """This library provides functions for manipulating Unicode strings and for
+ manipulating C strings according to the Unicode standard."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['827c1eb9cb6e7c738b171745dac0888aa58c5924df2e59239318383de0729b98']
+
+builddependencies = [
+    ('binutils', '2.35'),
+]
+
+parallel = 1
+
+sanity_check_paths = {
+    'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] +
+             ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm',
+                                              'stdio', 'str', 'types', 'wbrk', 'width']],
+    'dirs': ['include/unistring'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb
index d7c07a5167e..0b54a760099 100644
--- a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb
+++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb
@@ -35,7 +35,6 @@ dependencies = [
 
 configopts = "--with-pic --with-mpi --with-blas=openblas --with-lapack=openblas --without-gcc-arch "
 configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared "
-configopts += "LDFLAGS=$LDFLAGS+' -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lmpi_mpifh'"
 
 sanity_check_paths = {
     'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libpympb.a',

From bda2ad3b2ff00c3ad2197e75fb9ebeea4e7321d2 Mon Sep 17 00:00:00 2001
From: Arnold Kole <35299166+ahkole@users.noreply.github.com>
Date: Mon, 24 Apr 2023 12:33:09 +0200
Subject: [PATCH 413/601] Removed forcing of serial compilation

---
 .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb      | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
index 474990ff216..acb27067217 100644
--- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
+++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb
@@ -25,8 +25,6 @@ builddependencies = [
     ('pkgconf', '1.8.0'),
 ]
 
-parallel = 1
-
 sanity_check_paths = {
     'files': ['lib/libgridxc.a'],
     'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'],

From 688b26ab483b194bfadc14d8d47ce67d82c4a03c Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 24 Apr 2023 16:34:23 +0200
Subject: [PATCH 414/601] correctly disable some specific tests that cause
 problems on A40s

---
 .../c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb     | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
index ddafffc0fed..12a85d600f5 100644
--- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
+++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb
@@ -35,13 +35,17 @@ _skip_tests = [
     'tests/cupyx_tests/tools_tests',
     'tests/example_tests',
     'tests/cupy_tests/testing_tests/test_parameterized.py',
-    'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_',
     'tests/cupy_tests/fft_tests/test_fft.py',
+]
+_ignore_list = ' --ignore='.join(_skip_tests)
+
+_deselect_tests = [
+    'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_',
     # float16 has too low precision for these tests as they are written
     # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details.
     'tests/cupy_tests/linalg_tests/test_product.py::TestProduct',
 ]
-_ignore_list = ' --ignore='.join(_skip_tests)
+_deselect_list = ' --deselect='.join(_deselect_tests)
 
 exts_list = [
     ('fastrlock', '0.5', {
@@ -50,8 +54,8 @@ exts_list = [
     ('cupy', version, {
         # Must run tests here since the required version of pytest is a builddep
         # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory.
-        'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' %
-                   _ignore_list,
+        'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && '
+                   'pytest --ignore=%s --deselect=%s tests' % (_ignore_list, _deselect_list),
         'testinstall': True,
         'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'],
     }),

From b672bcf5fe754f10acee17692750dbb02d10d7c3 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Mon, 24 Apr 2023 16:58:35 +0200
Subject: [PATCH 415/601] adding easyconfigs: IsoSeq-3.8.2-linux-x86_64.eb

---
 .../i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb     | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb

diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
new file mode 100644
index 00000000000..7a7e2856fef
--- /dev/null
+++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
@@ -0,0 +1,25 @@
+easyblock = 'Binary'
+
+name = 'IsoSeq'
+version = '3.8.2'
+versionsuffix = '-linux-x86_64'
+
+homepage = 'https://github.com/PacificBiosciences/ioseq3'
+description = """IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added."""
+
+toolchain = SYSTEM
+
+source_urls = ["https://github.com/PacificBiosciences/%(namelower)s"]
+sources = ["releases/download/v%(version)s/%(namelower)s3"]
+checksums = ['3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7']
+
+extract_sources = False
+
+postinstallcmds = ["cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s"]
+
+sanity_check_paths = {
+    'files': ['isoseq3',],
+    'dirs': [''],
+}
+
+moduleclass = 'bio'
\ No newline at end of file

From b3c7596709b471eb0c38314b0305fa4bd6d27dc7 Mon Sep 17 00:00:00 2001
From: Leon Kos <leon.kos@lecad.fs.uni-lj.si>
Date: Mon, 24 Apr 2023 17:51:43 +0200
Subject: [PATCH 416/601] adding easyconfigs: GLI-4.5.31-GCCcore-10.2.0.eb,
 GLI-4.5.31-GCCcore-12.2.0.eb

---
 .../g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb        | 51 +++++++++++++++++++
 .../g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb        | 51 +++++++++++++++++++
 2 files changed, 102 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb
 create mode 100644 easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb
new file mode 100644
index 00000000000..7820338ddff
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb
@@ -0,0 +1,51 @@
+easyblock = "ConfigureMake"
+
+name = "GLI"
+version = "4.5.31"
+
+homepage = "https://pgi-jcns.fz-juelich.de/portal/pages/gli.html"
+description = "Graphics Language Interpreter"
+
+toolchain = {"name": "GCCcore", "version": "10.2.0"}
+toolchainopts = {"pic": True}
+
+source_urls = ["http://iffwww.iff.kfa-juelich.de/gli/"]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ["13b7def217672ab4fa01e39977af26f3fbbe0f7bbe7e7c42c2c4aa0ea5fc8c05"]
+
+builddependencies = [("binutils", "2.35")]
+
+dependencies = [
+    ('X11', '20201008'),
+    ('zlib', '1.2.11'),
+    ('Tk', '8.6.10'),
+    ('Tcl', '8.6.10'),
+    ('libtirpc', '1.3.1')
+]
+
+preconfigopts = 'cd src && '
+configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc '
+configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib'
+
+prebuildopts = 'cd src &&'
+
+preinstallopts = 'cd src &&'
+
+parallel = 1
+
+modextravars = {
+    "GLI_WSTYPE": "217",
+    "GLI_HOME": "%(installdir)s"
+}
+
+modextrapaths = {
+    "PATH": "",
+    "LD_LIBRARY_PATH": "",
+}
+
+sanity_check_paths = {
+    "files": ["libgks.a", "libgks.%s" % SHLIB_EXT, "libgli.a", "libgus.%s" % SHLIB_EXT],
+    "dirs": ["demo", "tcl/lib"],
+}
+
+moduleclass = "vis"
diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..68de3e62b7c
--- /dev/null
+++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb
@@ -0,0 +1,51 @@
+easyblock = "ConfigureMake"
+
+name = "GLI"
+version = "4.5.31"
+
+homepage = "https://pgi-jcns.fz-juelich.de/portal/pages/gli.html"
+description = "Graphics Language Interpreter"
+
+toolchain = {"name": "GCCcore", "version": "12.2.0"}
+toolchainopts = {"pic": True}
+
+source_urls = ["http://iffwww.iff.kfa-juelich.de/gli/"]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ["13b7def217672ab4fa01e39977af26f3fbbe0f7bbe7e7c42c2c4aa0ea5fc8c05"]
+
+builddependencies = [("binutils", "2.39")]
+
+dependencies = [
+    ('X11', '20221110'),
+    ('zlib', '1.2.12'),
+    ('Tk', '8.6.12'),
+    ('Tcl', '8.6.12'),
+    ('libtirpc', '1.3.3')
+]
+
+preconfigopts = 'cd src && '
+configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc '
+configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib'
+
+prebuildopts = 'cd src &&'
+
+preinstallopts = 'cd src &&'
+
+parallel = 1
+
+modextravars = {
+    "GLI_WSTYPE": "217",
+    "GLI_HOME": "%(installdir)s"
+}
+
+modextrapaths = {
+    "PATH": "",
+    "LD_LIBRARY_PATH": "",
+}
+
+sanity_check_paths = {
+    "files": ["libgks.a", "libgks.%s" % SHLIB_EXT, "libgli.a", "libgus.%s" % SHLIB_EXT],
+    "dirs": ["demo", "tcl/lib"],
+}
+
+moduleclass = "vis"

From 4ca82898f696db37ee6c512355a16e8d92b47374 Mon Sep 17 00:00:00 2001
From: Kim Serradell <kserradell@meteomatics.com>
Date: Tue, 25 Apr 2023 12:04:05 +0200
Subject: [PATCH 417/601] Replacing AOCC broken link

---
 easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb
index aca9ebc5b59..b2b557cf891 100644
--- a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb
@@ -8,7 +8,7 @@ description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0
 # already specified as the toolchain.
 toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
 
-source_urls = ['http://developer.amd.com/wordpress/media/files/']
+source_urls = ['https://download.amd.com/developer/eula/aocc-compiler/']
 sources = ['aocc-compiler-%(version)s.tar']
 checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4']
 

From 966a84ec6cd037be5aac904806dd904370a7dc95 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 25 Apr 2023 14:18:08 +0200
Subject: [PATCH 418/601] fix flatbuffers version

---
 .../pod5-file-format-0.1.8-foss-2022a.eb         |  4 ++--
 .../pod5-file-format-0.1.8_dep_fix.patch         | 16 +++++++++++-----
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
index 15436f8c712..5804c85e8ec 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
@@ -15,7 +15,7 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ
 patches = ['pod5-file-format-0.1.8_dep_fix.patch']
 checksums = [
     {'pod5-file-format-0.1.8.tar.gz': '262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'},
-    {'pod5-file-format-0.1.8_dep_fix.patch': 'd05e52467387c67bc87551eccbf5a6c3253ad1c4019eaf21ad861895e9a086c6'},
+    {'pod5-file-format-0.1.8_dep_fix.patch': 'd24fab7477d735ba7bb4a286c7a64d6138bf6a82a5a021b257eeeb5dfa06d82e'},
 ]
 
 builddependencies = [
@@ -28,7 +28,7 @@ dependencies = [
     ('Arrow', '8.0.0'),
     ('SciPy-bundle', '2022.05'),
     ('zstd', '1.5.2'),
-    ('flatbuffers', '2.0.0'),
+    ('flatbuffers', '2.0.7'),
     ('pybind11', '2.9.2'),
     ('Boost', '1.79.0'),
     ('build', '0.10.0'),
diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
index 2782bdeb102..f9430ef0310 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
@@ -1,12 +1,18 @@
 diff -u pod5-file-format-0.1.8/c++/CMakeLists.txt.orig pod5-file-format-0.1.8/c++/CMakeLists.txt
---- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig	2023-01-20 12:22:05.000000000 +0100
-+++ pod5-file-format-0.1.8/c++/CMakeLists.txt	2023-01-23 10:11:12.097686513 +0100
-@@ -21,6 +21,7 @@
+--- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig      2023-02-23 19:17:13.000000000 +0100
++++ pod5-file-format-0.1.8/c++/CMakeLists.txt   2023-04-25 14:07:28.174884834 +0200
+@@ -16,11 +16,12 @@
+         COMPONENTS
+             headers
+     )
+-    find_package(Flatbuffers REQUIRED)
++    find_package(FlatBuffers REQUIRED)
+     find_package(zstd REQUIRED)
  endif()
- 
+
  find_package(Threads REQUIRED)
 +find_package(pybind11 REQUIRED)
- 
+
  find_program(
      FLATBUFFERS_FLATC_EXECUTABLE
 diff -u pod5-file-format-0.1.8/CMakeLists.txt.orig pod5-file-format-0.1.8/CMakeLists.txt

From 12f781a6bcfc4e6d9530ac4e931a06db3e9f71de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 25 Apr 2023 14:36:39 +0200
Subject: [PATCH 419/601] add build easyconfig

---
 .../b/build/build-0.10.0-foss-2022a.eb        | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb
new file mode 100644
index 00000000000..ce8f9a50a22
--- /dev/null
+++ b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'build'
+version = '0.10.0'
+
+homepage = 'https://github.com/pypa/build'
+description = """A simple, correct Python build frontend."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pyparsing', '3.0.9', {
+        'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'],
+    }),
+    ('packaging', '20.4', {
+        'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'],
+    }),
+    ('tomli', '2.0.1', {
+        'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'],
+    }),
+    ('pyproject_hooks', '1.0.0', {
+        'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'],
+    }),
+    (name, version, {
+        'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'],
+    }),
+]
+
+sanity_check_commands = [
+    "python3 -m build -V",
+]
+
+moduleclass = 'devel'

From b0adb1c2ac2811c2dda57b95d87353753ded5dc4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Tue, 25 Apr 2023 14:38:33 +0200
Subject: [PATCH 420/601] remove unwanted file

---
 .../build-0.10.0-foss-2022a.eb                | 40 -------------------
 1 file changed, 40 deletions(-)
 delete mode 100644 easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb
deleted file mode 100644
index ce8f9a50a22..00000000000
--- a/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb
+++ /dev/null
@@ -1,40 +0,0 @@
-easyblock = 'PythonBundle'
-
-name = 'build'
-version = '0.10.0'
-
-homepage = 'https://github.com/pypa/build'
-description = """A simple, correct Python build frontend."""
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-dependencies = [
-    ('Python', '3.10.4'),
-]
-
-use_pip = True
-sanity_pip_check = True
-
-exts_list = [
-    ('pyparsing', '3.0.9', {
-        'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'],
-    }),
-    ('packaging', '20.4', {
-        'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'],
-    }),
-    ('tomli', '2.0.1', {
-        'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'],
-    }),
-    ('pyproject_hooks', '1.0.0', {
-        'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'],
-    }),
-    (name, version, {
-        'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'],
-    }),
-]
-
-sanity_check_commands = [
-    "python3 -m build -V",
-]
-
-moduleclass = 'devel'

From c20dade423b7e1d9c88a79cbe24188b0c7308be8 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Tue, 25 Apr 2023 15:18:20 +0200
Subject: [PATCH 421/601] adding easyconfigs: libRmath-4.2.1-GCCcore-11.3.0.eb

---
 .../libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..bd707d8a2e1
--- /dev/null
+++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb
@@ -0,0 +1,48 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# Updated: Denis Kristak (INUITS)
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+
+easyblock = 'ConfigureMake'
+
+name = 'libRmath'
+version = '4.2.1'
+
+homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library'
+description = """The routines supporting the distribution and special functions in R and a few others are declared
+ in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s']
+sources = ['R-%(version)s.tar.gz']
+checksums = ['4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('pkg-config', '0.29.2'),
+]
+dependencies = [
+    ('cURL', '7.83.0'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.2.5'),
+    ('zlib', '1.2.12'),
+    ('PCRE2', '10.40'),
+]
+
+preconfigopts = "cd %(builddir)s/R-%(version)s && "
+configopts = "--with-readline=no --with-recommended-packages=no --with-x=no"
+
+parallel = 1
+
+postinstallcmds = ['cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/']
+runtest = 'check'
+start_dir = 'src/nmath/standalone'
+
+sanity_check_paths = {
+    'files': ['lib/libRmaths.%s' % SHLIB_EXT, 'lib/%(name)s.a', 'lib/pkgconfig/%(name)s.pc', 'include/Rmath.h'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From 7ef647b926d6c82bece5f2cdf1f2cd6915f7fb7b Mon Sep 17 00:00:00 2001
From: easybuild <easybuild@rothhpc4-ezy.cluster.local>
Date: Tue, 25 Apr 2023 15:38:21 +0100
Subject: [PATCH 422/601] adding easyconfigs: Infernal-1.1.4-foss-2022b.eb

---
 .../i/Infernal/Infernal-1.1.4-foss-2022b.eb   | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb

diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb
new file mode 100644
index 00000000000..1f071f3e656
--- /dev/null
+++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb
@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'Infernal'
+version = "1.1.4"
+
+homepage = 'http://eddylab.org/infernal/'
+description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases
+ for RNA structure and sequence similarities."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['http://eddylab.org/%(namelower)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc']
+
+local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat']
+
+sanity_check_paths = {
+    'files': ['bin/cm%s' % x for x in local_bins],
+    'dirs': []
+}
+
+sanity_check_commands = ['cm%s -h' % x for x in local_bins]
+
+moduleclass = 'bio'

From f8b8db8d9b9a1249cf6ac8570d5a5a2e89399373 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Tue, 25 Apr 2023 16:47:11 +0200
Subject: [PATCH 423/601] adding easyconfigs: rgdal-1.6-6-foss-2022a-R-4.2.1.eb

---
 .../r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..168c2f06bc2
--- /dev/null
+++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,33 @@
+# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
+easyblock = 'RPackage'
+
+name = 'rgdal'
+version = '1.6-6'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://rgdal.r-forge.r-project.org/'
+description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and
+ access to projection/transformation operations from the 'PROJ.4' library."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+    'https://cran.r-project.org/src/contrib/',  # current version of packages
+    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+]
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['d742d7aadfc004771e61cac28a1faffeb4dbda981dea19115be11c541087399a']
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('GDAL', '3.5.0'),
+]
+
+
+sanity_check_paths = {
+    'files': ['%(name)s/R/%(name)s'],
+    'dirs': [],
+}
+
+moduleclass = 'geo'

From 2c8afe8b366004a39a8d286b1d33f9de6d459521 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Tue, 25 Apr 2023 18:18:47 +0200
Subject: [PATCH 424/601] Remove pointless version suffix, remove empty line.

---
 .../r/rgdal/rgdal-1.6-6-foss-2022a.eb         | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb

diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb
new file mode 100644
index 00000000000..9f53672f0cb
--- /dev/null
+++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb
@@ -0,0 +1,31 @@
+# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
+easyblock = 'RPackage'
+
+name = 'rgdal'
+version = '1.6-6'
+
+homepage = 'https://rgdal.r-forge.r-project.org/'
+description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and
+ access to projection/transformation operations from the 'PROJ.4' library."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+    'https://cran.r-project.org/src/contrib/',  # current version of packages
+    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+]
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['d742d7aadfc004771e61cac28a1faffeb4dbda981dea19115be11c541087399a']
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('GDAL', '3.5.0'),
+]
+
+sanity_check_paths = {
+    'files': ['%(name)s/R/%(name)s'],
+    'dirs': [],
+}
+
+moduleclass = 'geo'

From 7e156451bef9c4133b47cd37a47285b8c611cc18 Mon Sep 17 00:00:00 2001
From: easybuild <easybuild@rothhpc4-ezy.cluster.local>
Date: Tue, 25 Apr 2023 17:23:02 +0100
Subject: [PATCH 425/601] Copied in attribution and licence comments from
 previous versions, as per request of @verdurin.

---
 .../i/Infernal/Infernal-1.1.4-foss-2022b.eb         | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb
index 1f071f3e656..57d29e7b2b7 100644
--- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb
+++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb
@@ -1,3 +1,16 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis@cern.ch>
+# License::   MIT/GPL
+# Updated:: Denis Kristak (INUITS)
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
 easyblock = 'ConfigureMake'
 
 name = 'Infernal'

From 32ab02196e1f89f01506a31810e817bcfdf1944f Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Tue, 25 Apr 2023 18:26:04 +0200
Subject: [PATCH 426/601] Rename easyconfig, remove R version suffix.

---
 .../r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb | 33 -------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb
deleted file mode 100644
index 168c2f06bc2..00000000000
--- a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb
+++ /dev/null
@@ -1,33 +0,0 @@
-# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
-easyblock = 'RPackage'
-
-name = 'rgdal'
-version = '1.6-6'
-versionsuffix = '-R-%(rver)s'
-
-homepage = 'https://rgdal.r-forge.r-project.org/'
-description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and
- access to projection/transformation operations from the 'PROJ.4' library."""
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-source_urls = [
-    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-    'https://cran.r-project.org/src/contrib/',  # current version of packages
-    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-]
-sources = ['%(name)s_%(version)s.tar.gz']
-checksums = ['d742d7aadfc004771e61cac28a1faffeb4dbda981dea19115be11c541087399a']
-
-dependencies = [
-    ('R', '4.2.1'),
-    ('GDAL', '3.5.0'),
-]
-
-
-sanity_check_paths = {
-    'files': ['%(name)s/R/%(name)s'],
-    'dirs': [],
-}
-
-moduleclass = 'geo'

From 795a2807237a5e982d88ad01a8c23b5ac37529fb Mon Sep 17 00:00:00 2001
From: Ghepardo <ed.eyles@rothamsted.ac.uk>
Date: Tue, 25 Apr 2023 18:25:21 +0100
Subject: [PATCH 427/601] adding easyconfigs: tRNAscan-SE-2.0.12-foss-2022b.eb

---
 .../tRNAscan-SE-2.0.12-foss-2022b.eb          | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb

diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb
new file mode 100644
index 00000000000..f65eb9761f8
--- /dev/null
+++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'tRNAscan-SE'
+version = '2.0.12'
+
+homepage = 'http://trna.ucsc.edu/tRNAscan-SE/'
+description = """tRNAscan-SE is the most widely employed tool for identifying
+ and annotating tRNA genes in genomes."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['http://trna.ucsc.edu/software/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251']
+
+dependencies = [
+    ('Autoconf', '2.69', '', SYSTEM),
+    ('Infernal', '1.1.4'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/tRNAscan-SE',
+        'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm',
+    ],
+    'dirs': [
+        'bin',
+        'include',
+        'lib',
+    ],
+}
+
+# tRNAscan-SE.conf sets the Infernal bin directory to be ours.
+postinstallcmds = [
+    "for b in $(ls $EBROOTINFERNAL/bin); do ln -s $EBROOTINFERNAL/bin/$b %(installdir)s/bin; done",
+]
+
+moduleclass = 'bio'

From 9821440595d05123d0c8e28a80d32b2df2deaf64 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Tue, 25 Apr 2023 22:25:45 +0200
Subject: [PATCH 428/601] adding easyconfigs: muParser-2.3.4-GCCcore-11.3.0.eb

---
 .../muParser/muParser-2.3.4-GCCcore-11.3.0.eb | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..a5938bb05c3
--- /dev/null
+++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'CMakeMake'
+
+name = 'muParser'
+version = '2.3.4'
+
+homepage = 'https://beltoforion.de/article.php?a=muparser'
+description = """
+ muParser is an extensible high performance math expression parser library
+ written in C++. It works by transforming a mathematical expression into
+ bytecode and precalculating constant parts of the expression.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/beltoforion/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['0c3fa54a3ebf36dda0ed3e7cd5451c964afbb15102bdbcba08aafb359a290121']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+]
+
+configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON"
+
+
+sanity_check_paths = {
+    'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT ],
+    'dirs': [],
+}
+
+moduleclass = 'math'

From 789f22e9811d1290f1b9ccc98ef252085f425aa8 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Wed, 26 Apr 2023 08:28:20 +0200
Subject: [PATCH 429/601] Fix whitespace before square bracket.

---
 .../easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb
index a5938bb05c3..f20ab6b457e 100644
--- a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb
@@ -26,7 +26,7 @@ configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON"
 
 
 sanity_check_paths = {
-    'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT ],
+    'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT],
     'dirs': [],
 }
 

From b9bb9ef65899c8dcb33865555544dd2f172f5f26 Mon Sep 17 00:00:00 2001
From: Terje Kvernes <terje@kvernes.no>
Date: Wed, 26 Apr 2023 08:34:33 +0200
Subject: [PATCH 430/601] Fix sanity check after breaking it.

---
 .../easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb
index bd707d8a2e1..b8e5a2762f5 100644
--- a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb
@@ -41,7 +41,7 @@ runtest = 'check'
 start_dir = 'src/nmath/standalone'
 
 sanity_check_paths = {
-    'files': ['lib/libRmaths.%s' % SHLIB_EXT, 'lib/%(name)s.a', 'lib/pkgconfig/%(name)s.pc', 'include/Rmath.h'],
+    'files': ['lib/libRmath.%s' % SHLIB_EXT, 'lib/%(name)s.a', 'lib/pkgconfig/%(name)s.pc', 'include/Rmath.h'],
     'dirs': [],
 }
 

From dd0ee03b00d45729994216f4064966d08226f781 Mon Sep 17 00:00:00 2001
From: Bart te Lindert <bartt@uio.no>
Date: Wed, 26 Apr 2023 10:27:36 +0200
Subject: [PATCH 431/601] adding easyconfigs: rocm-smi-5.4.4-GCCcore-11.3.0.eb

---
 .../rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..adb4b6dc91d
--- /dev/null
+++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'rocm-smi'
+version = '5.4.4'
+
+homepage = 'https://github.com/RadeonOpenCompute/rocm_smi_lib'
+description = """The ROCm System Management Interface Library, or ROCm SMI
+library, is part of the Radeon Open Compute ROCm software stack. It is a C
+library for Linux that provides a user space interface for applications to
+monitor and control GPU applications."""
+docurls = ['https://rocmdocs.amd.com']
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ["https://github.com/RadeonOpenCompute/rocm_smi_lib/archive/"]
+sources = ["rocm-%(version)s.tar.gz"]
+checksums = ['27a6d851a493a3ab11ca3af079b4a0509579aa7bab2b2891af3bdf816a456ff0']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/rocm-smi'],
+    'dirs': [''],
+}
+
+sanity_check_commands = ['rocm-smi --help']
+
+moduleclass = 'tools'

From 2e996c9468e76e8aaf8d06d0d2c7bf4dca7a371b Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Wed, 26 Apr 2023 11:16:37 +0200
Subject: [PATCH 432/601] update to use final GCC 13.1.0 release

---
 ...GCCcore-13.0.1.eb => Bison-3.8.2-GCCcore-13.1.0.eb} |  4 ++--
 ...Ccore-13.0.1.eb => binutils-2.40-GCCcore-13.1.0.eb} |  2 +-
 ...-GCCcore-13.0.1.eb => flex-2.6.4-GCCcore-13.1.0.eb} |  6 +++---
 .../easyconfigs/g/GCC/{GCC-13.0.1.eb => GCC-13.1.0.eb} |  2 +-
 .../g/GCCcore/{GCCcore-13.0.1.eb => GCCcore-13.1.0.eb} | 10 +++-------
 ...ore-13.0.1.eb => help2man-1.49.3-GCCcore-13.1.0.eb} |  2 +-
 ...9-GCCcore-13.0.1.eb => M4-1.4.19-GCCcore-13.1.0.eb} |  2 +-
 ...GCCcore-13.0.1.eb => zlib-1.2.13-GCCcore-13.1.0.eb} |  7 ++-----
 8 files changed, 14 insertions(+), 21 deletions(-)
 rename easybuild/easyconfigs/b/Bison/{Bison-3.8.2-GCCcore-13.0.1.eb => Bison-3.8.2-GCCcore-13.1.0.eb} (88%)
 rename easybuild/easyconfigs/b/binutils/{binutils-2.40-GCCcore-13.0.1.eb => binutils-2.40-GCCcore-13.1.0.eb} (94%)
 rename easybuild/easyconfigs/f/flex/{flex-2.6.4-GCCcore-13.0.1.eb => flex-2.6.4-GCCcore-13.1.0.eb} (86%)
 rename easybuild/easyconfigs/g/GCC/{GCC-13.0.1.eb => GCC-13.1.0.eb} (97%)
 rename easybuild/easyconfigs/g/GCCcore/{GCCcore-13.0.1.eb => GCCcore-13.1.0.eb} (88%)
 rename easybuild/easyconfigs/h/help2man/{help2man-1.49.3-GCCcore-13.0.1.eb => help2man-1.49.3-GCCcore-13.1.0.eb} (91%)
 rename easybuild/easyconfigs/m/M4/{M4-1.4.19-GCCcore-13.0.1.eb => M4-1.4.19-GCCcore-13.1.0.eb} (94%)
 rename easybuild/easyconfigs/z/zlib/{zlib-1.2.13-GCCcore-13.0.1.eb => zlib-1.2.13-GCCcore-13.1.0.eb} (73%)

diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb
similarity index 88%
rename from easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb
rename to easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb
index 45f87974dc5..859d6c75e5a 100644
--- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb
+++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb
@@ -7,7 +7,7 @@ homepage = 'https://www.gnu.org/software/bison'
 description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar
  into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
@@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb']
 builddependencies = [
     ('M4', '1.4.19'),
     # use same binutils version that was used when building GCCcore toolchain
-    ('binutils', '2.39', '', SYSTEM),
+    ('binutils', '2.40', '', SYSTEM),
 ]
 
 
diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb
similarity index 94%
rename from easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb
rename to easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb
index 36234b61ea1..10be685a805 100644
--- a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb
+++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb
@@ -4,7 +4,7 @@ version = '2.40'
 homepage = 'https://directory.fsf.org/project/binutils/'
 description = "binutils: GNU binary utilities"
 
-toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCE_TAR_GZ]
diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb
similarity index 86%
rename from easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb
rename to easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb
index e4b6d071111..6d11a9f3e06 100644
--- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb
+++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb
@@ -1,7 +1,7 @@
 name = 'flex'
 version = '2.6.4'
 
-homepage = 'http://flex.sourceforge.net/'
+homepage = 'https://github.com/westes/flex'
 
 description = """
  Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,
@@ -9,7 +9,7 @@ description = """
  in text.
 """
 
-toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/']
@@ -20,7 +20,7 @@ builddependencies = [
     ('Bison', '3.8.2'),
     ('help2man', '1.49.3'),
     # use same binutils version that was used when building GCC toolchain
-    ('binutils', '2.39', '', SYSTEM),
+    ('binutils', '2.40', '', SYSTEM),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb b/easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb
similarity index 97%
rename from easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb
rename to easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb
index b9c224ad66e..8bf33a423ce 100644
--- a/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb
+++ b/easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'Bundle'
 
 name = 'GCC'
-version = '13.0.1'
+version = '13.1.0'
 
 homepage = 'https://gcc.gnu.org/'
 description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb
similarity index 88%
rename from easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb
rename to easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb
index 0b8d30d3782..3493e06b275 100644
--- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb
+++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'EB_GCC'
 
 name = 'GCCcore'
-version = '13.0.1'
+version = '13.1.0'
 
 homepage = 'https://gcc.gnu.org/'
 description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
@@ -22,11 +22,7 @@ source_urls = [
     'https://github.com/MentorEmbedded/nvptx-tools/archive',  # for nvptx-tools
 ]
 sources = [
-    {
-        'source_urls': ['https://gcc.gnu.org/pub/gcc/snapshots/13.1.0-RC2-20230419/'],
-        'filename': 'gcc-13.1.0-RC2-20230419.tar.gz',
-    },
-    # 'gcc-%(version)s.tar.gz',
+    'gcc-%(version)s.tar.gz',
     'gmp-6.2.1.tar.bz2',
     'mpfr-4.1.0.tar.bz2',
     'mpc-1.2.1.tar.gz',
@@ -39,7 +35,7 @@ patches = [
     'GCCcore-9.3.0_gmp-c99.patch',
 ]
 checksums = [
-    {'gcc-13.1.0-RC2-20230419.tar.gz': '31188ab89af2b52fc5e3a2ef77c52d4b762e18320b3d741fa947e3d0dd306134'},
+    {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'},
     {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'},
     {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'},
     {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'},
diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb
similarity index 91%
rename from easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb
rename to easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb
index 92adccec4f1..7cf3afc6f6c 100644
--- a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb
+++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb
@@ -6,7 +6,7 @@ version = '1.49.3'
 homepage = 'https://www.gnu.org/software/help2man/'
 description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCE_TAR_XZ]
diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb
similarity index 94%
rename from easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb
rename to easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb
index 6a458ba47b3..88a7a87c4dc 100644
--- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb
+++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb
@@ -8,7 +8,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce
   although it has some extensions (for example, handling more than 9 positional parameters to macros).
  GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 
 source_urls = [GNU_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb
similarity index 73%
rename from easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb
rename to easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb
index 32d9c8ca56c..082092433d1 100644
--- a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb
+++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb
@@ -8,16 +8,13 @@ description = """zlib is designed to be a free, general-purpose, legally unencum
  not covered by any patents -- lossless data-compression library for use on virtually any
  computer hardware and operating system."""
 
-toolchain = {'name': 'GCCcore', 'version': '13.0.1'}
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 toolchainopts = {'pic': True}
 
 source_urls = ['https://zlib.net/fossils']
 sources = [SOURCELOWER_TAR_GZ]
 # patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch']
-checksums = [
-    'b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30',  # zlib-1.2.12.tar.gz
-    # 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238',  # zlib-1.2.12_fix-CC-logic-in-configure.patch
-]
+checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30']
 
 # use same binutils version that was used when building GCC toolchain
 builddependencies = [('binutils', '2.40', '', SYSTEM)]

From cb81b83c1ce952633b84b9131faae943c4b8cbef Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Wed, 26 Apr 2023 11:24:25 +0200
Subject: [PATCH 433/601] use correct binutils version

---
 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb
index 88a7a87c4dc..5f8b9df7e74 100644
--- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb
+++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb
@@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ]
 checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70']
 
 # use same binutils version that was used when building GCC toolchain
-builddependencies = [('binutils', '2.39', '', SYSTEM)]
+builddependencies = [('binutils', '2.40', '', SYSTEM)]
 
 # '-fgnu89-inline' is required to avoid linking errors with older glibc's,
 # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529

From 3d53a0d73f9966d7fbf14768a0e60525173f2598 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 26 Apr 2023 12:26:51 +0200
Subject: [PATCH 434/601] blacked to solve formatting issues

---
 .../i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb     | 24 +++++++++++--------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
index 7a7e2856fef..0acc15a6486 100644
--- a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
@@ -1,25 +1,29 @@
-easyblock = 'Binary'
+easyblock = "Binary"
 
-name = 'IsoSeq'
-version = '3.8.2'
-versionsuffix = '-linux-x86_64'
+name = "IsoSeq"
+version = "3.8.2"
+versionsuffix = "-linux-x86_64"
 
-homepage = 'https://github.com/PacificBiosciences/ioseq3'
+homepage = "https://github.com/PacificBiosciences/ioseq3"
 description = """IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added."""
 
 toolchain = SYSTEM
 
 source_urls = ["https://github.com/PacificBiosciences/%(namelower)s"]
 sources = ["releases/download/v%(version)s/%(namelower)s3"]
-checksums = ['3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7']
+checksums = ["3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7"]
 
 extract_sources = False
 
-postinstallcmds = ["cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s"]
+postinstallcmds = [
+    "cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s"
+]
 
 sanity_check_paths = {
-    'files': ['isoseq3',],
-    'dirs': [''],
+    "files": [
+        "isoseq3",
+    ],
+    "dirs": [""],
 }
 
-moduleclass = 'bio'
\ No newline at end of file
+moduleclass = "bio"

From 2ec32b7cbeefdb44171e3f0715e7e9eef80c9392 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Wed, 26 Apr 2023 13:42:32 +0200
Subject: [PATCH 435/601] adding easyconfigs:
 GitPython-3.1.31-GCCcore-12.2.0.eb

---
 .../GitPython-3.1.31-GCCcore-12.2.0.eb        | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..84adb82aa2e
--- /dev/null
+++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonBundle'
+
+name = 'GitPython'
+version = '3.1.31'
+
+homepage = 'https://gitpython.readthedocs.org'
+description = """ GitPython is a python library used to interact with Git repositories """
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('git', '2.38.1', '-nodocs'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('smmap', '5.0.0', {
+        'checksums': ['c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936'],
+    }),
+    ('gitdb', '4.0.10', {
+        'checksums': ['6eb990b69df4e15bad899ea868dc46572c3f75339735663b81de79b06f17eb9a'],
+    }),
+    (name, version, {
+        'modulename': 'git',
+        'checksums': ['8ce3bcf69adfdf7c7d503e78fd3b1c492af782d58893b650adb2ac8912ddd573'],
+    }),
+]
+
+moduleclass = 'lib'

From dfe0c0fb516dd92c90144673cdc8f56b0fae3a3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 26 Apr 2023 14:18:01 +0200
Subject: [PATCH 436/601] adding easyconfigs: ncurses-6.4-GCCcore-13.1.0.eb,
 bzip2-1.0.8-GCCcore-13.1.0.eb, cURL-8.0.1-GCCcore-13.1.0.eb,
 XZ-5.4.2-GCCcore-13.1.0.eb, libarchive-3.6.2-GCCcore-13.1.0.eb,
 CMake-3.26.3-GCCcore-13.1.0.eb

---
 .../b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb     | 27 +++++++++++
 .../c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb    | 30 ++++++++++++
 .../c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb       | 43 +++++++++++++++++
 .../libarchive-3.6.2-GCCcore-13.1.0.eb        | 33 +++++++++++++
 .../n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb   | 47 +++++++++++++++++++
 .../x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb           | 34 ++++++++++++++
 6 files changed, 214 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb

diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..e719f5aa433
--- /dev/null
+++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb
@@ -0,0 +1,27 @@
+name = 'bzip2'
+version = '1.0.8'
+
+homepage = 'https://sourceware.org/bzip2'
+description = """
+ bzip2 is a freely available, patent free, high-quality data compressor. It
+ typically compresses files to within 10% to 15% of the best available
+ techniques (the PPM family of statistical compressors), whilst being around
+ twice as fast at compression and six times faster at decompression.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://sourceware.org/pub/%(name)s/']
+sources = [SOURCE_TAR_GZ]
+patches = ['bzip2-%(version)s-pkgconfig.patch']
+checksums = [
+    'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269',  # bzip2-1.0.8.tar.gz
+    '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1',  # bzip2-1.0.8-pkgconfig.patch
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..ce03c3694cd
--- /dev/null
+++ b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb
@@ -0,0 +1,30 @@
+name = 'CMake'
+version = '3.26.3'
+
+homepage = 'https://www.cmake.org'
+
+description = """
+ CMake, the cross-platform, open-source build system.  CMake is a family of
+ tools designed to build, test and package software.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+
+source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('cURL', '8.0.1'),
+    ('libarchive', '3.6.2'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..10cd7fbe3f2
--- /dev/null
+++ b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb
@@ -0,0 +1,43 @@
+easyblock = 'ConfigureMake'
+
+name = 'cURL'
+version = '8.0.1'
+
+homepage = 'https://curl.haxx.se'
+
+description = """
+ libcurl is a free and easy-to-use client-side URL transfer library,
+ supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP,
+ LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP.
+ libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP
+ form based upload, proxies, cookies, user+password authentication (Basic,
+ Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling
+ and more.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+
+source_urls = ['https://curl.haxx.se/download/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5fd29000a4089934f121eff456101f0a5d09e2a3e89da1d714adf06c4be887cb']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+configopts = '--with-zlib '
+configopts += '--with-ssl=$EBROOTOPENSSL '
+
+modextravars = {'CURL_INCLUDES': '%(installdir)s/include'}
+
+sanity_check_paths = {
+    'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig', 'include/curl'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..f0260cb95ae
--- /dev/null
+++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'libarchive'
+version = '3.6.2'
+
+homepage = 'https://www.libarchive.org/'
+
+description = """
+ Multi-format archive and compression library
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+
+source_urls = ['https://www.libarchive.org/downloads/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('XZ', '5.4.2'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'share/man/man3'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..edca9ab5954
--- /dev/null
+++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb
@@ -0,0 +1,47 @@
+easyblock = 'ConfigureMake'
+
+name = 'ncurses'
+version = '6.4'
+
+homepage = 'https://www.gnu.org/software/ncurses/'
+description = """
+ The Ncurses (new curses) library is a free software emulation of curses in
+ System V Release 4.0, and more. It uses Terminfo format, supports pads and
+ color and multiple highlights and forms characters and function-key mapping,
+ and has all the other SYSV-curses enhancements over BSD Curses.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159']
+
+builddependencies = [('binutils', '2.40')]
+
+local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms "
+configopts = [
+    # build ncurses: serial build in default paths with shared libraries
+    local_common_configopts,
+    # build ncursesw: serial with UTF-8
+    local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/",
+]
+
+# Symlink libtinfo to libncurses
+# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically
+postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done']
+
+_target_suffix = ['', 'w']  # '': ncurses, 'w': ncursesw
+_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]]
+_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config",
+                                     "reset", "tabs", "tic", "toe", "tput", "tset"]] +
+             ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] +
+             ['lib/libncurses++%s.a' % x for x in _target_suffix],
+    'dirs': ['include', 'include/ncursesw'],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..ffee85b04a3
--- /dev/null
+++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'XZ'
+version = '5.4.2'
+
+homepage = 'https://tukaani.org/xz/'
+description = "xz: XZ utilities"
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+
+source_urls = ['https://tukaani.org/xz/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['aa49909cbd9028c4666a35fa4975f9a6203ed98154fbb8223ee43ef9ceee97c3']
+
+builddependencies = [
+    # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ)
+    ('gettext', '0.21.1', '', SYSTEM),
+    ('binutils', '2.40'),
+]
+
+# may become useful in non-x86 archs
+# configopts = ' --disable-assembler '
+
+sanity_check_paths = {
+    'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "xz --help",
+    "unxz --help",
+]
+
+moduleclass = 'tools'

From eddba5189bb751e5c319fce339ab217e12d9bcb4 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Wed, 26 Apr 2023 14:23:29 +0200
Subject: [PATCH 437/601] adding easyconfigs: pyperf-2.6.0-GCCcore-12.2.0.eb

---
 .../p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb   | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..2cc5f691e4a
--- /dev/null
+++ b/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonPackage'
+
+name = 'pyperf'
+version = '2.6.0'
+
+homepage = 'https://github.com/psf/pyperf'
+description = "The Python pyperf module is a toolkit to write, run and analyze benchmarks"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['d7e367a1ec7035d7a2b25f55a5925596c00cb15851f28cffd85b05b7307232af']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': ['bin/pyperf'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["pyperf --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From d3b605a96402cf4befb5436f3046c9376d32ca1e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 26 Apr 2023 14:36:49 +0200
Subject: [PATCH 438/601] adding easyconfigs: pkgconf-1.9.4-GCCcore-13.1.0.eb

---
 .../p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb

diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..6e817cde0bd
--- /dev/null
+++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'pkgconf'
+version = '1.9.4'
+
+homepage = 'https://github.com/pkgconf/pkgconf'
+
+description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries.
+ It is similar to pkg-config from freedesktop.org."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+
+source_urls = ['https://distfiles.dereferenced.org/pkgconf/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d6b844ab6bf8ca685e9ef8103dee64fb39b2484c7a18da64ae5ba269514c9f78']
+
+builddependencies = [('binutils', '2.40')]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"]
+
+sanity_check_paths = {
+    'files': ['bin/pkg-config', 'bin/pkgconf'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "pkg-config --help",
+    "pkgconf --help",
+]
+
+moduleclass = 'devel'

From 40f28d899009ae3cc95b3887d1e3d3841b3f47a5 Mon Sep 17 00:00:00 2001
From: Christian Meesters <meesters@uni-mainz.de>
Date: Wed, 26 Apr 2023 15:16:28 +0200
Subject: [PATCH 439/601] blacked to solve formatting issues - once more

---
 .../easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
index 0acc15a6486..7a5b7acf67a 100644
--- a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
@@ -5,7 +5,16 @@ version = "3.8.2"
 versionsuffix = "-linux-x86_64"
 
 homepage = "https://github.com/PacificBiosciences/ioseq3"
-description = """IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added."""
+description = """IsoSeq v3 contains the newest tools to identify transcripts
+                 in PacBio single-molecule sequencing data. Starting in SMRT 
+                 Link v6.0.0, those tools power the IsoSeq GUI-based analysis 
+                 application. A composable workflow of existing tools and
+                 algorithms, combined with a new clustering technique, allows
+                 to process the ever-increasing yield of PacBio machines with
+                 similar performance to IsoSeq versions 1 and 2. Starting with 
+                 version 3.4, support for UMI and cell barcode based 
+                 deduplication has been added.
+                 """
 
 toolchain = SYSTEM
 

From 9ef8c8599cf564bd5a9d1f0de0f6e64237993b90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 26 Apr 2023 18:53:28 +0200
Subject: [PATCH 440/601] adding easyconfigs: Tcl-8.6.13-GCCcore-13.1.0.eb,
 UnZip-6.0-GCCcore-13.1.0.eb, libreadline-8.2-GCCcore-13.1.0.eb,
 SQLite-3.41.2-GCCcore-13.1.0.eb, libffi-3.4.4-GCCcore-13.1.0.eb

---
 .../l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb   | 29 +++++++++
 .../libreadline-8.2-GCCcore-13.1.0.eb         | 41 +++++++++++++
 .../s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb  | 39 ++++++++++++
 .../t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb        | 41 +++++++++++++
 .../u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb       | 59 +++++++++++++++++++
 5 files changed, 209 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb
 create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb

diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..d64748fec2e
--- /dev/null
+++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'libffi'
+version = '3.4.4'
+
+homepage = 'https://sourceware.org/libffi/'
+description = """The libffi library provides a portable, high level programming interface to
+ various calling conventions. This allows a programmer to call any function
+ specified by a call interface description at run-time."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+configopts = '--disable-exec-static-tramp '
+
+sanity_check_paths = {
+    'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..2c0323f20bf
--- /dev/null
+++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'libreadline'
+version = '8.2'
+
+homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html'
+description = """
+ The GNU Readline library provides a set of functions for use by applications
+ that allow users to edit command lines as they are typed in. Both Emacs and
+ vi editing modes are available. The Readline library includes additional
+ functions to maintain a list of previously-entered command lines, to recall
+ and perhaps reedit those lines, and perform csh-like history expansion on
+ previous commands.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://ftp.gnu.org/gnu/readline']
+sources = ['readline-%(version)s.tar.gz']
+checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('ncurses', '6.4'),
+]
+
+# for the termcap symbols, use EB ncurses
+buildopts = "SHLIB_LIBS='-lncurses'"
+
+sanity_check_paths = {
+    'files': ['lib/libreadline.a', 'lib/libhistory.a'] +
+             ['include/readline/%s' % x
+              for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h',
+                        'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..4ea12e5cf78
--- /dev/null
+++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'SQLite'
+version = '3.41.2'
+local_filename_version = '3410200'
+
+homepage = 'https://www.sqlite.org/'
+description = "SQLite: SQL Database Engine in a C Library"
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.sqlite.org/2023/']
+sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)]
+checksums = ['e98c100dd1da4e30fa460761dab7c0b91a50b785e167f8c57acc46514fae9499']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('libreadline', '8.2'),
+    ('Tcl', '8.6.13'),
+]
+
+# enable additional APIs that provide access to meta-data about tables and queries
+# needed for GDAL when it used as a dep for QGIS
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"'
+
+sanity_check_paths = {
+    'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h',
+              'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig'],
+}
+
+sanity_check_commands = [
+    'sqlite3 --version | grep ^%(version)s',
+]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..f8906b46e22
--- /dev/null
+++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'Tcl'
+version = '8.6.13'
+
+homepage = 'https://www.tcl.tk/'
+description = """
+ Tcl (Tool Command Language) is a very powerful but easy to learn dynamic
+ programming language, suitable for a very wide range of uses, including web
+ and desktop applications, networking, administration, testing and many more.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+
+source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s']
+sources = ['%(namelower)s%(version)s-src.tar.gz']
+checksums = ['e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"'
+
+runtest = 'test'
+
+start_dir = 'unix'
+
+postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh']
+
+sanity_check_paths = {
+    'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh',
+              'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT,
+              'lib/tclConfig.sh', 'man/man1/tclsh.1'],
+    'dirs': ['share'],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb
new file mode 100644
index 00000000000..bfb9b30c73c
--- /dev/null
+++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb
@@ -0,0 +1,59 @@
+easyblock = 'ConfigureMake'
+
+name = 'UnZip'
+version = '6.0'
+
+homepage = 'http://www.info-zip.org/UnZip.html'
+description = """UnZip is an extraction utility for archives compressed
+in .zip format (also called "zipfiles"). Although highly compatible both
+with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's
+own Zip program, our primary objectives have been portability and
+non-MSDOS functionality."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
+
+source_urls = ['https://download.sourceforge.net/infozip']
+sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz']
+patches = [
+    'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch',
+]
+checksums = [
+    '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37',  # unzip60.tar.gz
+    # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch
+    '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe',
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+]
+
+skipsteps = ['configure']
+
+local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT'
+            '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD',
+            '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT']
+
+buildopts = ' '.join([
+    "-f unix/Makefile",
+    'CC="$CC"',
+    'D_USE_BZ2=-DUSE_BZIP2',
+    'L_BZ2=-lbz2',
+    'LF2="$LDFLAGS"',
+    'CF="%s"' % ' '.join(local_cf),
+    'unzips',
+])
+
+installopts = '-f unix/Makefile prefix=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/unzip', 'bin/zipinfo'],
+    'dirs': ['man/man1']
+}
+
+sanity_check_commands = ["unzip -v"]
+
+moduleclass = 'tools'

From 7cdf4ef12498bdbc30c9ebb0f96da5d02efa89fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 26 Apr 2023 19:02:02 +0200
Subject: [PATCH 441/601] Fix checksum for tcl

---
 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb
index f8906b46e22..172e6387099 100644
--- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb
+++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb
@@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.1.0'}
 
 source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s']
 sources = ['%(namelower)s%(version)s-src.tar.gz']
-checksums = ['e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855']
+checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066']
 
 builddependencies = [
     ('binutils', '2.40'),

From 5fa1cea38525a007bc67eec28fd19812d09a90b7 Mon Sep 17 00:00:00 2001
From: Christian Meesters <cmeesters@users.noreply.github.com>
Date: Thu, 27 Apr 2023 10:59:38 +0200
Subject: [PATCH 442/601] Update
 easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb

Co-authored-by: Adam Huffman <verdurin@users.noreply.github.com>
---
 easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
index 7a5b7acf67a..5e8f0c47b88 100644
--- a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
+++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb
@@ -35,4 +35,6 @@ sanity_check_paths = {
     "dirs": [""],
 }
 
+sanity_check_commands = ['isoseq3 --version']
+
 moduleclass = "bio"

From 0bf969f0db1548097e5b283d23f3f458f8c918a1 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:15:43 +0200
Subject: [PATCH 443/601] adding easyconfigs: coverage-7.2.3-GCCcore-12.2.0.eb

---
 .../coverage/coverage-7.2.3-GCCcore-12.2.0.eb | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..724f8c3da15
--- /dev/null
+++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonPackage'
+
+name = 'coverage'
+version = '7.2.3'
+
+homepage = 'https://coverage.readthedocs.io'
+description = """ Coverage.py is a tool for measuring code coverage of Python programs.
+ It monitors your program, noting which parts of the code have been executed,
+ then analyzes the source to identify code that could have been executed but was not. """
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['d298c2815fa4891edd9abe5ad6e6cb4207104c7dd9fd13aea3fdebf6f9b91259']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+sanity_check_paths = {
+    'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
+}
+
+moduleclass = 'tools'

From c7e9fcd8c17a1a3e23eebd9ec442a291863155bc Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:23:11 +0200
Subject: [PATCH 444/601] adding easyconfigs: PyTables-3.8.0-foss-2022b.eb

---
 .../p/PyTables/PyTables-3.8.0-foss-2022b.eb   | 74 +++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb
new file mode 100644
index 00000000000..82fda5ef075
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb
@@ -0,0 +1,74 @@
+# http://www.pytables.org/usersguide/installation.html
+# updated: Denis Kristak (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'PyTables'
+version = '3.8.0'
+
+homepage = 'https://www.pytables.org'
+description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope
+ with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the
+ NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical
+ parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing,
+ processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and 
+ disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions 
+ such as relational or object oriented databases."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'usempi': True}
+
+builddependencies = [
+    ('pkgconf', '1.9.3'),
+    ('CMake', '3.24.3'),
+    ('Ninja', '1.11.1'),
+    ('scikit-build', '0.17.2'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),  # provides numexpr
+    ('HDF5', '1.14.0'),
+    ('LZO', '2.10'),
+    ('Blosc', '1.21.3'),
+    ('Blosc2', '2.8.0'),
+    ('py-cpuinfo', '9.0.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('blosc2', '2.0.0', {
+        'patches': ['blosc2-2.0.0_use-Blosc2-dep.patch'],
+        'checksums': [
+            {'blosc2-2.0.0.tar.gz': 'f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'},
+            {'blosc2-2.0.0_use-Blosc2-dep.patch': '6a9443f378472ada3c8fe8a8a346fe16f22b01bab7d9e60c23b64b546178054b'},
+        ],
+    }),
+    ('tables', version, {
+        'patches': [
+            'PyTables-%(version)s_fix-libs.patch',
+            'PyTables-3.8.0_fix-find-blosc2-library-path.patch',
+        ],
+        'checksums': [
+            {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'},
+            {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'},
+            {'PyTables-3.8.0_fix-find-blosc2-library-path.patch':
+             'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'},
+        ],
+    }),
+]
+
+local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree']
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+options = {'modulename': 'tables'}
+
+sanity_check_commands = ["%s --help" % x for x in local_bins]
+
+sanity_pip_check = True
+
+moduleclass = 'data'

From 2cf5df89b02c953abc4328dec43bfd1b13a9d7e5 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:28:34 +0200
Subject: [PATCH 445/601] adding easyconfigs: PyGEOS-0.14-gfbf-2022b.eb

---
 .../p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb        | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb

diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb
new file mode 100644
index 00000000000..28d542d1710
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'PyGEOS'
+version = '0.14'
+
+homepage = "https://pygeos.readthedocs.io"
+description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in
+ the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance
+ improvement when operating on arrays of geometries."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['30fbc17f64844200b85133b885fcfb65541b8779531f6ef4f8fe467d3fba7623']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('GEOS', '3.11.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+moduleclass = 'geo'

From e4dc506ee19265c7eb71da6da57d6a7fda4517eb Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:29:36 +0200
Subject: [PATCH 446/601] adding easyconfigs:
 netcdf4-python-1.6.3-foss-2022b.eb

---
 .../netcdf4-python-1.6.3-foss-2022b.eb        | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb

diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb
new file mode 100644
index 00000000000..ef656081b80
--- /dev/null
+++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb
@@ -0,0 +1,57 @@
+easyblock = 'PythonBundle'
+
+name = 'netcdf4-python'
+version = '1.6.3'
+
+homepage = 'https://unidata.github.io/netcdf4-python/'
+description = """Python/numpy interface to netCDF."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+toolchainopts = {'usempi': True}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('netCDF', '4.9.0'),
+    ('cURL', '7.86.0'),
+    ('mpi4py', '3.1.4'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('cftime', '1.6.2', {
+        'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'],
+    }),
+    (name, version, {
+        'patches': [
+            'netcdf4-python-1.1.8-avoid-diskless-test.patch',
+            'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch',
+        ],
+        'source_tmpl': 'netCDF4-%(version)s.tar.gz',
+        'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'],
+        'checksums': [
+            {'netCDF4-1.6.3.tar.gz': '8c98a3a8cda06920ee8bd24a71226ddf0328c22bd838b0afca9cb45fb4580d99'},
+            {'netcdf4-python-1.1.8-avoid-diskless-test.patch':
+             'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72'},
+            {'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch':
+             '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166'},
+        ],
+    }),
+]
+
+fix_python_shebang_for = ['bin/*']
+
+sanity_check_paths = {
+    'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "nc4tonc3 --help",
+    "nc3tonc4 --help",
+    "ncinfo --help",
+]
+
+moduleclass = 'data'

From 17604bd08f25e6dddeb8f114df24b81da94e2310 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:30:42 +0200
Subject: [PATCH 447/601] adding easyconfigs: lxml-4.9.2-GCCcore-12.2.0.eb

---
 .../l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb       | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..20323870198
--- /dev/null
+++ b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'lxml'
+version = '4.9.2'
+
+homepage = 'https://lxml.de/'
+description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['2455cfaeb7ac70338b3257f41e21f0724f4b5b0c0e7702da67ee6c3640835b67']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('libxml2', '2.10.3'),
+    ('libxslt', '1.1.37'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'lib'

From c9462d49d8e13362aa927a0ae35787c41c409a66 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Thu, 27 Apr 2023 15:47:13 +0200
Subject: [PATCH 448/601] scikit-build/0.17.2, Blosc/1.21.3, Blosc2/2.8.0,
 py-cpuinfo/9.0.0 for GCCcore/12.2.0

---
 .../b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb    | 28 +++++++++++++
 .../b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb   | 31 +++++++++++++++
 .../py-cpuinfo-9.0.0-GCCcore-12.2.0.eb        | 39 +++++++++++++++++++
 .../scikit-build-0.17.2-GCCcore-12.2.0.eb     | 33 ++++++++++++++++
 4 files changed, 131 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..a3e524a900f
--- /dev/null
+++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Blosc'
+version = '1.21.3'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+source_urls = ['https://github.com/Blosc/c-blosc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['941016c4564bca662080bb01aea74f06630bd665e598c6f6967fd91b2e2e0bb6']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a',
+              'lib/libblosc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..8eb833b9f41
--- /dev/null
+++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb
@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Blosc2'
+version = '2.8.0'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++11'}
+
+source_urls = ['https://github.com/Blosc/c-blosc2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['be608cdf68deb02e0d3ee62e183942a0fe5d5d3185375b9b6566e2ae35a9bdbd']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a',
+              'lib/libblosc2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..a36d83f17ab
--- /dev/null
+++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'PythonPackage'
+
+name = 'py-cpuinfo'
+version = '9.0.0'
+
+homepage = 'https://github.com/workhorsy/py-cpuinfo'
+description = "py-cpuinfo gets CPU info with pure Python."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': ['bin/cpuinfo'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "cpuinfo",
+    "python -m cpuinfo",
+]
+
+options = {'modulename': 'cpuinfo'}
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..ed4f8e89aff
--- /dev/null
+++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'PythonBundle'
+
+name = 'scikit-build'
+version = '0.17.2'
+
+homepage = 'https://scikit-build.readthedocs.io/en/latest'
+description = """Scikit-Build, or skbuild, is an improved build system generator
+for CPython C/C++/Fortran/Cython extensions."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('distro', '1.8.0', {
+        'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'],
+    }),
+    ('scikit_build', version, {
+        'modulename': 'skbuild',
+        'checksums': ['348cfd2137c68cbf9fa589ed74fd07b0340a65a1888e2481cfc63356485188a6'],
+    }),
+]
+
+moduleclass = 'lib'

From 93e913272139930011a83e8724c2d4e9d747852a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 28 Apr 2023 11:27:24 +0200
Subject: [PATCH 449/601] adding easyconfigs: bcbio-gff-0.7.0-foss-2020b.eb

---
 .../b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb

diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb
new file mode 100644
index 00000000000..66fc839020b
--- /dev/null
+++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb
@@ -0,0 +1,42 @@
+# Contribution by
+# DeepThought, Flinders University
+# Updated to v0.6.7
+# R.QIAO <rob.qiao@flinders.edu.au>
+
+easyblock = 'PythonPackage'
+
+name = 'bcbio-gff'
+version = '0.7.0'
+
+homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff'
+
+description = """
+Read and write Generic Feature Format (GFF) with Biopython integration.
+"""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d']
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('Biopython', '1.78'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages'
+local_targets = ['GFFOutput.py', 'GFFParser.py']
+
+sanity_check_paths = {
+    'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets],
+    'dirs': [local_bcbiogffroot],
+}
+
+options = {'modulename': 'BCBio.GFF'}
+
+moduleclass = 'bio'

From 67de0c2e182236bd2723a1e331c300e96bd22051 Mon Sep 17 00:00:00 2001
From: Bart te Lindert <bartt@uio.no>
Date: Fri, 28 Apr 2023 13:12:09 +0200
Subject: [PATCH 450/601] adding easyconfigs: BAMM-2.5.0-foss-2022a.eb

---
 .../b/BAMM/BAMM-2.5.0-foss-2022a.eb           | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb
new file mode 100644
index 00000000000..023f4d53608
--- /dev/null
+++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb
@@ -0,0 +1,29 @@
+easyblock = 'CMakeMake'
+
+name = 'BAMM'
+version = '2.5.0'
+
+homepage = 'http://bamm-project.org/'
+description = """ BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. 
+It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of 
+lineage diversification and trait evolution. """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': True}
+
+# https://github.com/macroevolution/bamm
+github_account = 'macroevolution'
+# source_urls = ['https://github.com/macroevolution/bamm/archive']
+source_urls = ['GITHUB_LOWER_SOURCE']
+sources = ['v%(version)s.tar.gz']
+checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4']
+
+builddependencies = [('CMake', '3.23.1')]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+sanity_check_commands = ["%(namelower)s"]
+
+moduleclass = 'bio'

From 618489ae9eb03eb44ba84a92d1e6d082aab890aa Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Fri, 28 Apr 2023 14:28:12 +0000
Subject: [PATCH 451/601] adding easyconfigs: ont-guppy-6.4.8-CUDA-11.7.0.eb

---
 .../ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb  | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb
new file mode 100644
index 00000000000..65649652d4d
--- /dev/null
+++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb
@@ -0,0 +1,38 @@
+# Author: Jasper Grimm (UoY)
+easyblock = 'Tarball'
+
+name = 'ont-guppy'
+version = '6.4.8'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol'
+description = """
+Guppy is a bioinformatics toolkit that enables real-time basecalling and several
+ post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms.
+
+ For Research Use Only
+"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis']
+sources = ['%(name)s_%(version)s_linux64.tar.gz']
+checksums = ['d58aba66b1b29180946ecacf3f7b423a6933db5d12aeda783485b1ee82fd110b']
+
+dependencies = [
+    ('CUDA', '11.7.0'),
+]
+
+_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex',
+                                  'basecaller_supervisor', 'basecall_server']]
+_libs = ['lib/libvbz_hdf_plugin.a']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in _bins] + _libs,
+    'dirs': ['data'],
+}
+
+# requires libcuda.so to be present, else it exits with code 127
+# sanity_check_commands = ['%s --help' % x for x in _bins]
+
+moduleclass = 'bio'

From ad2d8a50d44b7eb248fb628febdf45efe86d10c5 Mon Sep 17 00:00:00 2001
From: Leon Kos <leon.kos@lecad.fs.uni-lj.si>
Date: Fri, 28 Apr 2023 16:55:35 +0200
Subject: [PATCH 452/601] Fix ZLIB linking

---
 easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb | 2 ++
 easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb
index 7820338ddff..ca2a334a1af 100644
--- a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb
@@ -24,7 +24,9 @@ dependencies = [
 ]
 
 preconfigopts = 'cd src && '
+preconfigopts += 'sed -i -e "/ac_cv_c_zlib=.*with_zlib/s,},}/libz.so," configure && '
 configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc '
+configopts += '--with-zlib=$EBROOTZLIB/lib --with-zlibinclude=$EBROOTZLIB/include '
 configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib'
 
 prebuildopts = 'cd src &&'
diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb
index 68de3e62b7c..5f8d5037d42 100644
--- a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb
@@ -24,7 +24,9 @@ dependencies = [
 ]
 
 preconfigopts = 'cd src && '
+preconfigopts += 'sed -i -e "/ac_cv_c_zlib=.*with_zlib/s,},}/libz.so," configure && '
 configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc '
+configopts += '--with-zlib=$EBROOTZLIB/lib --with-zlibinclude=$EBROOTZLIB/include '
 configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib'
 
 prebuildopts = 'cd src &&'

From 6426027275789c39f47c54c31f991af5f478881d Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Fri, 28 Apr 2023 16:13:10 +0100
Subject: [PATCH 453/601] specify source_urls inside exts_default_options to
 ensure correct name expansion for the archivedd packages

---
 .../Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb  | 18 ++++++++----------
 .../Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb  | 17 ++++++++---------
 .../Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb  | 15 ++++++++-------
 .../Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb  | 15 ++++++++-------
 .../Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb  | 15 ++++++++-------
 5 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb
index be3f28cdb22..0489f0e3fcf 100644
--- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb
+++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb
@@ -9,37 +9,35 @@ description = "Seurat is an R package designed for QC, analysis, and exploration
 
 toolchain = {'name': 'foss', 'version': '2020b'}
 
-source_urls = [
-    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-    'https://cran.r-project.org/src/contrib/',  # current version of packages
-    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-]
-
 dependencies = [
     ('R', '4.0.3'),
     ('R-bundle-Bioconductor', '3.12', versionsuffix),
 ]
 
 exts_defaultclass = 'RPackage'
-exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']}
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
 
 exts_list = [
     ('spatstat.utils', '2.1-0', {
-        'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.utils'],
         'checksums': ['ed3569fea295b62396c49cdcfe476414b0b0f3e52044175532f316a402d3f8a1'],
     }),
     ('spatstat.data', '2.1-0', {
         'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'],
     }),
     ('spatstat.geom', '2.0-1', {
-        'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'],
         'checksums': ['70ebfe115e733b2e6778baf6e2935861472154c0dd21f15a84ec2a61e0a3f6e4'],
     }),
     ('spatstat.sparse', '2.0-0', {
         'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'],
     }),
     ('spatstat.core', '2.0-0', {
-        'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'],
         'checksums': ['fde9a91bd32b7a3c8b25e802a16d470dcc919c24da5715149e1d91eeec119ba7'],
     }),
     (name, version, {
diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb
index d71472a2d5e..b8a228157b7 100644
--- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb
+++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb
@@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration
 
 toolchain = {'name': 'foss', 'version': '2020b'}
 
-source_urls = [
-    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-    'https://cran.r-project.org/src/contrib/',  # current version of packages
-    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-]
-
 dependencies = [
     ('R', '4.0.3'),
     ('R-bundle-Bioconductor', '3.12', versionsuffix),
 ]
 
 exts_defaultclass = 'RPackage'
-exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']}
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
 
 exts_list = [
     ('spatstat.utils', '2.2-0', {
@@ -31,14 +32,12 @@ exts_list = [
         'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'],
     }),
     ('spatstat.geom', '2.2-0', {
-        'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'],
         'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'],
     }),
     ('spatstat.sparse', '2.0-0', {
         'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'],
     }),
     ('spatstat.core', '2.2-0', {
-        'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'],
         'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'],
     }),
     ('Matrix', '1.3-4', {
diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb
index af03c570285..19cfccaecdc 100644
--- a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb
+++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb
@@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
-source_urls = [
-    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-    'https://cran.r-project.org/src/contrib/',  # current version of packages
-    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-]
-
 dependencies = [
     ('R', '4.2.1'),
     ('R-bundle-Bioconductor', '3.15', versionsuffix),
 ]
 
 exts_defaultclass = 'RPackage'
-exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']}
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
 
 exts_list = [
     ('Matrix', '1.5-1', {
diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb
index b98250be5b3..fe25468c3f6 100644
--- a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb
+++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb
@@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration
 
 toolchain = {'name': 'foss', 'version': '2021b'}
 
-source_urls = [
-    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-    'https://cran.r-project.org/src/contrib/',  # current version of packages
-    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-]
-
 dependencies = [
     ('R', '4.1.2'),
     ('R-bundle-Bioconductor', '3.14', versionsuffix),
 ]
 
 exts_defaultclass = 'RPackage'
-exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']}
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
 
 exts_list = [
     ('Matrix', '1.5-3', {
diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb
index 3529ca55994..032d6c672cd 100644
--- a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb
+++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb
@@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
-source_urls = [
-    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-    'https://cran.r-project.org/src/contrib/',  # current version of packages
-    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-]
-
 dependencies = [
     ('R', '4.2.1'),
     ('R-bundle-Bioconductor', '3.15', versionsuffix),
 ]
 
 exts_defaultclass = 'RPackage'
-exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']}
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
 
 exts_list = [
     ('Matrix', '1.5-4', {

From 04b54c5cfec69df6ae9e3ee70d69683cb9f5c36c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 1 May 2023 01:06:27 +0200
Subject: [PATCH 454/601] adding easyconfigs:
 Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb

---
 ...-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb | 456 ++++++++++++++++++
 1 file changed, 456 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb

diff --git a/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb
new file mode 100644
index 00000000000..b3535b944b2
--- /dev/null
+++ b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb
@@ -0,0 +1,456 @@
+easyblock = 'Cargo'
+
+name = 'Evcxr-REPL'
+version = '0.14.2'
+local_rustver = '1.65.0'
+versionsuffix = '-Rust-' + local_rustver
+
+homepage = 'https://github.com/evcxr'
+description = "A Rust REPL (Read-Eval-Print loop) built using the evcxr evaluation context."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+crates = [
+    ('evcxr_repl',  version),
+    ('evcxr', version),
+    ('addr2line', '0.19.0'),
+    ('adler', '1.0.2'),
+    ('always-assert', '0.1.2'),
+    ('ansi_term', '0.12.1'),
+    ('anyhow', '1.0.68'),
+    ('anymap', '1.0.0-beta.2'),
+    ('ariadne', '0.1.5'),
+    ('arrayvec', '0.7.2'),
+    ('atty', '0.2.14'),
+    ('autocfg', '1.1.0'),
+    ('backtrace', '0.3.67'),
+    ('bitflags', '1.3.2'),
+    ('camino', '1.1.1'),
+    ('cargo-platform', '0.1.2'),
+    ('cargo_metadata', '0.15.2'),
+    ('cc', '1.0.78'),
+    ('cfg-if', '1.0.0'),
+    ('chalk-derive', '0.88.0'),
+    ('chalk-ir', '0.88.0'),
+    ('chalk-recursive', '0.88.0'),
+    ('chalk-solve', '0.88.0'),
+    ('clap', '2.34.0'),
+    ('clipboard-win', '4.4.2'),
+    ('colored', '2.0.0'),
+    ('countme', '3.0.1'),
+    ('cov-mark', '2.0.0-pre.1'),
+    ('crossbeam-channel', '0.5.6'),
+    ('crossbeam-deque', '0.8.2'),
+    ('crossbeam-epoch', '0.9.13'),
+    ('crossbeam-utils', '0.8.14'),
+    ('ctrlc', '3.2.4'),
+    ('dashmap', '5.4.0'),
+    ('dirs', '4.0.0'),
+    ('dirs-next', '2.0.0'),
+    ('dirs-sys', '0.3.7'),
+    ('dirs-sys-next', '0.1.2'),
+    ('dissimilar', '1.0.5'),
+    ('dot', '0.1.4'),
+    ('drop_bomb', '0.1.5'),
+    ('either', '1.8.0'),
+    ('ena', '0.14.0'),
+    ('endian-type', '0.1.2'),
+    ('errno', '0.2.8'),
+    ('errno-dragonfly', '0.1.2'),
+    ('error-code', '2.3.1'),
+    ('evcxr_input', '1.0.0'),
+    ('fastrand', '1.8.0'),
+    ('fd-lock', '3.0.8'),
+    ('filetime', '0.2.19'),
+    ('fixedbitset', '0.2.0'),
+    ('form_urlencoded', '1.1.0'),
+    ('fsevent-sys', '4.1.0'),
+    ('fst', '0.4.7'),
+    ('getrandom', '0.2.8'),
+    ('gimli', '0.27.0'),
+    ('hashbrown', '0.12.3'),
+    ('heck', '0.3.3'),
+    ('hermit-abi', '0.1.19'),
+    ('hermit-abi', '0.2.6'),
+    ('hkalbasi-rustc-ap-rustc_abi', '0.0.20221221'),
+    ('hkalbasi-rustc-ap-rustc_index', '0.0.20221221'),
+    ('home', '0.5.4'),
+    ('idna', '0.3.0'),
+    ('indexmap', '1.9.2'),
+    ('inotify', '0.9.6'),
+    ('inotify-sys', '0.1.5'),
+    ('instant', '0.1.12'),
+    ('io-lifetimes', '1.0.3'),
+    ('itertools', '0.10.5'),
+    ('itoa', '1.0.5'),
+    ('jod-thread', '0.1.2'),
+    ('json', '0.12.4'),
+    ('kqueue', '1.0.7'),
+    ('kqueue-sys', '1.0.3'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.139'),
+    ('libloading', '0.7.4'),
+    ('libmimalloc-sys', '0.1.28'),
+    ('linux-raw-sys', '0.1.4'),
+    ('lock_api', '0.4.9'),
+    ('log', '0.4.17'),
+    ('memchr', '2.5.0'),
+    ('memoffset', '0.6.5'),
+    ('memoffset', '0.7.1'),
+    ('mimalloc', '0.1.32'),
+    ('miniz_oxide', '0.6.2'),
+    ('mio', '0.8.5'),
+    ('miow', '0.5.0'),
+    ('nibble_vec', '0.1.0'),
+    ('nix', '0.24.3'),
+    ('nix', '0.26.1'),
+    ('notify', '5.0.0'),
+    ('num_cpus', '1.15.0'),
+    ('object', '0.30.0'),
+    ('once_cell', '1.17.0'),
+    ('oorandom', '11.1.3'),
+    ('parking_lot', '0.11.2'),
+    ('parking_lot', '0.12.1'),
+    ('parking_lot_core', '0.8.6'),
+    ('parking_lot_core', '0.9.5'),
+    ('percent-encoding', '2.2.0'),
+    ('perf-event', '0.4.8'),
+    ('perf-event-open-sys', '4.0.0'),
+    ('petgraph', '0.5.1'),
+    ('pin-project-lite', '0.2.9'),
+    ('proc-macro-error', '1.0.4'),
+    ('proc-macro-error-attr', '1.0.4'),
+    ('proc-macro2', '1.0.49'),
+    ('pulldown-cmark', '0.9.2'),
+    ('pulldown-cmark-to-cmark', '10.0.4'),
+    ('quote', '1.0.23'),
+    ('ra_ap_base_db', '0.0.145'),
+    ('ra_ap_cfg', '0.0.145'),
+    ('ra_ap_hir', '0.0.145'),
+    ('ra_ap_hir_def', '0.0.145'),
+    ('ra_ap_hir_expand', '0.0.145'),
+    ('ra_ap_hir_ty', '0.0.145'),
+    ('ra_ap_ide', '0.0.145'),
+    ('ra_ap_ide_assists', '0.0.145'),
+    ('ra_ap_ide_completion', '0.0.145'),
+    ('ra_ap_ide_db', '0.0.145'),
+    ('ra_ap_ide_diagnostics', '0.0.145'),
+    ('ra_ap_ide_ssr', '0.0.145'),
+    ('ra_ap_la-arena', '0.0.145'),
+    ('ra_ap_limit', '0.0.145'),
+    ('ra_ap_mbe', '0.0.145'),
+    ('ra_ap_parser', '0.0.145'),
+    ('ra_ap_paths', '0.0.145'),
+    ('ra_ap_profile', '0.0.145'),
+    ('ra_ap_project_model', '0.0.145'),
+    ('ra_ap_stdx', '0.0.145'),
+    ('ra_ap_syntax', '0.0.145'),
+    ('ra_ap_test_utils', '0.0.145'),
+    ('ra_ap_text_edit', '0.0.145'),
+    ('ra_ap_toolchain', '0.0.145'),
+    ('ra_ap_tt', '0.0.145'),
+    ('ra_ap_vfs', '0.0.145'),
+    ('ra_ap_vfs-notify', '0.0.145'),
+    ('radix_trie', '0.2.1'),
+    ('rayon', '1.6.1'),
+    ('rayon-core', '1.10.1'),
+    ('redox_syscall', '0.2.16'),
+    ('redox_users', '0.4.3'),
+    ('regex', '1.7.0'),
+    ('regex-syntax', '0.6.28'),
+    ('remove_dir_all', '0.5.3'),
+    ('rowan', '0.15.10'),
+    ('rustc-ap-rustc_lexer', '725.0.0'),
+    ('rustc-demangle', '0.1.21'),
+    ('rustc-hash', '1.1.0'),
+    ('rustix', '0.36.6'),
+    ('rustyline', '10.0.0'),
+    ('ryu', '1.0.12'),
+    ('salsa', '0.17.0-pre.2'),
+    ('salsa-macros', '0.17.0-pre.2'),
+    ('same-file', '1.0.6'),
+    ('scoped-tls', '1.0.1'),
+    ('scopeguard', '1.1.0'),
+    ('semver', '1.0.16'),
+    ('serde', '1.0.152'),
+    ('serde_derive', '1.0.152'),
+    ('serde_json', '1.0.91'),
+    ('sig', '1.0.0'),
+    ('smallvec', '1.10.0'),
+    ('smol_str', '0.1.23'),
+    ('static_assertions', '1.1.0'),
+    ('str-buf', '1.0.6'),
+    ('strsim', '0.8.0'),
+    ('structopt', '0.3.26'),
+    ('structopt-derive', '0.4.18'),
+    ('syn', '1.0.107'),
+    ('synstructure', '0.12.6'),
+    ('tempfile', '3.3.0'),
+    ('text-size', '1.1.0'),
+    ('textwrap', '0.11.0'),
+    ('thiserror', '1.0.38'),
+    ('thiserror-impl', '1.0.38'),
+    ('tinyvec', '1.6.0'),
+    ('tinyvec_macros', '0.1.0'),
+    ('tracing', '0.1.37'),
+    ('tracing-attributes', '0.1.23'),
+    ('tracing-core', '0.1.30'),
+    ('typed-arena', '2.0.1'),
+    ('unicase', '2.6.0'),
+    ('unicode-bidi', '0.3.8'),
+    ('unicode-ident', '1.0.6'),
+    ('unicode-normalization', '0.1.22'),
+    ('unicode-segmentation', '1.10.0'),
+    ('unicode-width', '0.1.10'),
+    ('unicode-xid', '0.2.4'),
+    ('url', '2.3.1'),
+    ('utf8parse', '0.2.0'),
+    ('vec_map', '0.8.2'),
+    ('version_check', '0.9.4'),
+    ('walkdir', '2.3.2'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('which', '4.3.0'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-util', '0.1.5'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-sys', '0.42.0'),
+    ('windows_aarch64_gnullvm', '0.42.0'),
+    ('windows_aarch64_msvc', '0.42.0'),
+    ('windows_i686_gnu', '0.42.0'),
+    ('windows_i686_msvc', '0.42.0'),
+    ('windows_x86_64_gnu', '0.42.0'),
+    ('windows_x86_64_gnullvm', '0.42.0'),
+    ('windows_x86_64_msvc', '0.42.0'),
+    ('yansi', '0.5.1'),
+]
+sources = []
+checksums = [
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+    {'crossbeam-channel-0.5.6.tar.gz': 'c2dd04ddaf88237dc3b8d8f9a3c1004b506b54b3313403944054d23c0870c521'},
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+    {'crossbeam-utils-0.8.14.tar.gz': '4fb766fa798726286dbbb842f174001dab8abc7b627a1dd86e0b7222a95d929f'},
+    {'ctrlc-3.2.4.tar.gz': '1631ca6e3c59112501a9d87fd86f21591ff77acd31331e8a73f8d80a65bbdd71'},
+    {'dashmap-5.4.0.tar.gz': '907076dfda823b0b36d2a1bb5f90c96660a5bbcd7729e10727f07858f22c4edc'},
+    {'dirs-4.0.0.tar.gz': 'ca3aa72a6f96ea37bbc5aa912f6788242832f75369bdfdadcb0e38423f100059'},
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+    {'dissimilar-1.0.5.tar.gz': 'bd5f0c7e4bd266b8ab2550e6238d2e74977c23c15536ac7be45e9c95e2e3fbbb'},
+    {'dot-0.1.4.tar.gz': 'a74b6c4d4a1cff5f454164363c16b72fa12463ca6b31f4b5f2035a65fa3d5906'},
+    {'drop_bomb-0.1.5.tar.gz': '9bda8e21c04aca2ae33ffc2fd8c23134f3cac46db123ba97bd9d3f3b8a4a85e1'},
+    {'either-1.8.0.tar.gz': '90e5c1c8368803113bf0c9584fc495a58b86dc8a29edbf8fe877d21d9507e797'},
+    {'ena-0.14.0.tar.gz': 'd7402b94a93c24e742487327a7cd839dc9d36fec9de9fb25b09f2dae459f36c3'},
+    {'endian-type-0.1.2.tar.gz': 'c34f04666d835ff5d62e058c3995147c06f42fe86ff053337632bca83e42702d'},
+    {'errno-0.2.8.tar.gz': 'f639046355ee4f37944e44f60642c6f3a7efa3cf6b78c78a0d989a8ce6c396a1'},
+    {'errno-dragonfly-0.1.2.tar.gz': 'aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf'},
+    {'error-code-2.3.1.tar.gz': '64f18991e7bf11e7ffee451b5318b5c1a73c52d0d0ada6e5a3017c8c1ced6a21'},
+    {'evcxr_input-1.0.0.tar.gz': '15ed7e9b5d7d7506798f5154e9e6390a08a0d4fff03835247a4f423041059a78'},
+    {'fastrand-1.8.0.tar.gz': 'a7a407cfaa3385c4ae6b23e84623d48c2798d06e3e6a1878f7f59f17b3f86499'},
+    {'fd-lock-3.0.8.tar.gz': 'bb21c69b9fea5e15dbc1049e4b77145dd0ba1c84019c488102de0dc4ea4b0a27'},
+    {'filetime-0.2.19.tar.gz': '4e884668cd0c7480504233e951174ddc3b382f7c2666e3b7310b5c4e7b0c37f9'},
+    {'fixedbitset-0.2.0.tar.gz': '37ab347416e802de484e4d03c7316c48f1ecb56574dfd4a46a80f173ce1de04d'},
+    {'form_urlencoded-1.1.0.tar.gz': 'a9c384f161156f5260c24a097c56119f9be8c798586aecc13afbcbe7b7e26bf8'},
+    {'fsevent-sys-4.1.0.tar.gz': '76ee7a02da4d231650c7cea31349b889be2f45ddb3ef3032d2ec8185f6313fd2'},
+    {'fst-0.4.7.tar.gz': '7ab85b9b05e3978cc9a9cf8fea7f01b494e1a09ed3037e16ba39edc7a29eb61a'},
+    {'getrandom-0.2.8.tar.gz': 'c05aeb6a22b8f62540c194aac980f2115af067bfe15a0734d7277a768d396b31'},
+    {'gimli-0.27.0.tar.gz': 'dec7af912d60cdbd3677c1af9352ebae6fb8394d165568a2234df0fa00f87793'},
+    {'hashbrown-0.12.3.tar.gz': '8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888'},
+    {'heck-0.3.3.tar.gz': '6d621efb26863f0e9924c6ac577e8275e5e6b77455db64ffa6c65c904e9e132c'},
+    {'hermit-abi-0.1.19.tar.gz': '62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33'},
+    {'hermit-abi-0.2.6.tar.gz': 'ee512640fe35acbfb4bb779db6f0d80704c2cacfa2e39b601ef3e3f47d1ae4c7'},
+    {'hkalbasi-rustc-ap-rustc_abi-0.0.20221221.tar.gz':
+     'adabaadad9aa7576f97af02241cdf5554d62fb3d51a84cb05d77ba28edd3013f'},
+    {'hkalbasi-rustc-ap-rustc_index-0.0.20221221.tar.gz':
+     'f4d3c48474e09afb0f5efbd6f758e05411699301a113c47d454d28ec7059d00e'},
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+    {'walkdir-2.3.2.tar.gz': '808cf2735cd4b6866113f648b791c6adc5714537bc222d9347bb203386ffda56'},
+    {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'},
+    {'which-4.3.0.tar.gz': '1c831fbbee9e129a8cf93e7747a82da9d95ba8e16621cae60ec2cdc849bacb7b'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'windows-sys-0.42.0.tar.gz': '5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7'},
+    {'windows_aarch64_gnullvm-0.42.0.tar.gz': '41d2aa71f6f0cbe00ae5167d90ef3cfe66527d6f613ca78ac8024c3ccab9a19e'},
+    {'windows_aarch64_msvc-0.42.0.tar.gz': 'dd0f252f5a35cac83d6311b2e795981f5ee6e67eb1f9a7f64eb4500fbc4dcdb4'},
+    {'windows_i686_gnu-0.42.0.tar.gz': 'fbeae19f6716841636c28d695375df17562ca208b2b7d0dc47635a50ae6c5de7'},
+    {'windows_i686_msvc-0.42.0.tar.gz': '84c12f65daa39dd2babe6e442988fc329d6243fdce47d7d2d155b8d874862246'},
+    {'windows_x86_64_gnu-0.42.0.tar.gz': 'bf7b1b21b5362cbc318f686150e5bcea75ecedc74dd157d874d754a2ca44b0ed'},
+    {'windows_x86_64_gnullvm-0.42.0.tar.gz': '09d525d2ba30eeb3297665bd434a54297e4170c7f1a44cad4ef58095b4cd2028'},
+    {'windows_x86_64_msvc-0.42.0.tar.gz': 'f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5'},
+    {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'},
+]
+
+dependencies = [
+    ('Rust', local_rustver),
+]
+
+sanity_check_paths = {
+    'files': ['bin/evcxr'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["evcxr --help"]
+
+moduleclass = 'tools'

From b29995e8200602e5895b165c6bbcd5dcd502e0bb Mon Sep 17 00:00:00 2001
From: Bart te Lindert <bartt@uio.no>
Date: Mon, 1 May 2023 09:40:18 +0200
Subject: [PATCH 455/601] remove single quotes

---
 easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb
index 023f4d53608..9fe5174b287 100644
--- a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb
@@ -13,8 +13,7 @@ toolchainopts = {'usempi': True}
 
 # https://github.com/macroevolution/bamm
 github_account = 'macroevolution'
-# source_urls = ['https://github.com/macroevolution/bamm/archive']
-source_urls = ['GITHUB_LOWER_SOURCE']
+source_urls = [GITHUB_LOWER_SOURCE]
 sources = ['v%(version)s.tar.gz']
 checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4']
 

From 7e7a359704a4608043f2bea2170ed9e520d38e43 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 2 May 2023 11:23:39 +0200
Subject: [PATCH 456/601] adding easyconfigs: EZC3D-1.5.2-foss-2022a.eb

---
 .../e/EZC3D/EZC3D-1.5.2-foss-2022a.eb         | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb

diff --git a/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb
new file mode 100644
index 00000000000..e7880604adc
--- /dev/null
+++ b/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb
@@ -0,0 +1,39 @@
+easyblock = "CMakePythonPackage"
+
+name = 'EZC3D'
+version = '1.5.2'
+
+homepage = 'https://pyomeca.github.io/Documentation/ezc3d/index.html'
+description = """EZC3D is an easy to use reader, modifier and writer for C3D format files. It is
+written en C++ with proper binders for Python and MATLAB/Octave scripting
+langages."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+github_account = 'pyomeca'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['Release_%(version)s.tar.gz']
+checksums = ['469c2089c0f885c9dd994bb02d70939da1ec2ddd37ea353964aafa8a5b2d7165']
+
+builddependencies = {
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),
+    ('SWIG', '4.0.2'),
+}
+
+dependencies = {
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+}
+
+# enable Python bindings
+_py_install_dir = "%(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s"
+configopts = "-DBINDER_PYTHON3=ON "
+configopts += "-DPYTHON_INSTALL_PREFIX=%s" % _py_install_dir
+
+sanity_check_paths = {
+    'files': ['lib/libezc3d.%s' % SHLIB_EXT],
+    'dirs': ['include/ezc3d', _py_install_dir],
+}
+
+moduleclass = 'lib'

From 45e2023300aa74f4173ce91ba122441e13ef8934 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 2 May 2023 11:29:04 +0200
Subject: [PATCH 457/601] adding easyconfigs: h5netcdf-1.1.0-foss-2021b.eb

---
 .../h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb   | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb

diff --git a/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb
new file mode 100644
index 00000000000..7efee9efd0a
--- /dev/null
+++ b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb
@@ -0,0 +1,27 @@
+easyblock = 'PythonBundle'
+
+name = 'h5netcdf'
+version = '1.1.0'
+
+homepage = 'https://h5netcdf.org/'
+description = """A Python interface for the netCDF4 file-format that reads and writes local or
+remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata
+netCDF library."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+dependencies = [
+    ('Python', '3.9.6'),
+    ('h5py', '3.6.0'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['932c3b573bed7370ebfc9e802cd60f1a4da5236efb11b36eeff897324d76bf56'],
+    }),
+]
+
+moduleclass = 'data'

From c7ae9b1d4b12e700e5eaaa3694d9525c790dbbd5 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 2 May 2023 11:25:32 +0200
Subject: [PATCH 458/601] adding easyconfigs:
 batchgenerators-0.25-foss-2021a.eb,
 HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb, HD-BET-20220318-foss-2021a.eb

---
 .../batchgenerators-0.25-foss-2021a.eb        | 30 ++++++++++++++++
 .../HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb | 34 +++++++++++++++++++
 .../h/HD-BET/HD-BET-20220318-foss-2021a.eb    | 32 +++++++++++++++++
 3 files changed, 96 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb
 create mode 100644 easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb
 create mode 100644 easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb

diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb
new file mode 100644
index 00000000000..8fc66740160
--- /dev/null
+++ b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb
@@ -0,0 +1,30 @@
+easyblock = 'PythonPackage'
+
+name = 'batchgenerators'
+version = '0.25'
+
+homepage = 'https://github.com/MIC-DKFZ/batchgenerators'
+description = """Data augmentation toolkit developed at the Division of Medical
+Image Computing at the German Cancer Research Center (DKFZ) to suit all our
+deep learning data augmentation needs."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['38a67413e847ff367e64abac36331fcb065494202d526ae96f7644de3a0e5495']
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('scikit-image', '0.18.3'),
+    ('scikit-learn', '0.24.2'),
+]
+
+# remove requirement on Pillow and unittest2, which are not actually used
+preinstallopts = "sed -i '13d;19d' setup.py &&"
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb
new file mode 100644
index 00000000000..0b7aef32343
--- /dev/null
+++ b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb
@@ -0,0 +1,34 @@
+easyblock = 'PythonPackage'
+
+name = 'HD-BET'
+version = '20220318'
+versionsuffix = '-CUDA-%(cudaver)s'
+_commit = '56c7fb8e6509563aa6377cdb0f2dd4e7ad359252'
+
+homepage = 'https://github.com/MIC-DKFZ/HD-BET'
+description = "Tool for brain extraction."
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+github_account = 'MIC-DKFZ'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%s.tar.gz' % _commit]
+checksums = ['744eb7b084feefb4243855529537a47fa4d1c1d93b6b967969c2ede8b9b8b46a']
+
+dependencies = [
+    ('CUDA', '11.3.1', '', SYSTEM),
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('PyTorch', '1.10.0', versionsuffix),
+    ('scikit-image', '0.18.3'),
+    ('SimpleITK', '2.1.1'),
+    ('batchgenerators', '0.25'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': 'HD_BET'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb
new file mode 100644
index 00000000000..e671387837e
--- /dev/null
+++ b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb
@@ -0,0 +1,32 @@
+easyblock = 'PythonPackage'
+
+name = 'HD-BET'
+version = '20220318'
+_commit = '56c7fb8e6509563aa6377cdb0f2dd4e7ad359252'
+
+homepage = 'https://github.com/MIC-DKFZ/HD-BET'
+description = "Tool for brain extraction."
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+github_account = 'MIC-DKFZ'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%s.tar.gz' % _commit]
+checksums = ['744eb7b084feefb4243855529537a47fa4d1c1d93b6b967969c2ede8b9b8b46a']
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('PyTorch', '1.10.0'),
+    ('scikit-image', '0.18.3'),
+    ('SimpleITK', '2.1.1'),
+    ('batchgenerators', '0.25'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+options = {'modulename': 'HD_BET'}
+
+moduleclass = 'bio'

From a0ea025a9c06474f005cd3a0e63fd699b1d701a9 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 2 May 2023 13:43:51 +0200
Subject: [PATCH 459/601] adding easyconfigs:
 python-docx-0.8.11-GCCcore-12.2.0.eb

---
 .../python-docx-0.8.11-GCCcore-12.2.0.eb      | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..4dc389d5dc9
--- /dev/null
+++ b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'PythonPackage'
+
+name = 'python-docx'
+version = '0.8.11'
+
+homepage = 'https://python-docx.readthedocs.io/en/latest/'
+description = 'python-docx is a Python library for creating and updating Microsoft Word (.docx) files'
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['1105d233a0956dd8dd1e710d20b159e2d72ac3c301041b95f4d4ceb3e0ebebc4']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('lxml', '4.9.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+options = {'modulename': 'docx'}
+
+moduleclass = 'tools'

From 4b031244095230c28cc9b4ce2a128605502e13ec Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 2 May 2023 13:49:09 +0200
Subject: [PATCH 460/601] adding easyconfigs: trimesh-3.21.5-gfbf-2022b.eb

---
 .../t/trimesh/trimesh-3.21.5-gfbf-2022b.eb    | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb

diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb
new file mode 100644
index 00000000000..b0321430d59
--- /dev/null
+++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb
@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'trimesh'
+version = '3.21.5'
+
+homepage = 'https://trimsh.org/'
+description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on
+watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy
+manipulation and analysis, in the style of the excellent Polygon object in the Shapely library."""
+
+toolchain = {'name': 'gfbf', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['74741bc7f9fcb94b98951db8dc8ec8364a2ef52ac2ca0761c7ba06182ef329be']
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),  # numpy required
+]
+
+moduleclass = 'lib'

From 509d547095a608e4de580fa96bac037abf6ac21d Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Tue, 2 May 2023 13:15:41 +0100
Subject: [PATCH 461/601] add Doxygen build dependency to X11

---
 easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb  | 1 +
 easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb  | 1 +
 easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb | 1 +
 easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb | 1 +
 easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb | 1 +
 easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb | 1 +
 easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb | 1 +
 7 files changed, 7 insertions(+)

diff --git a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb
index 21b4362d798..44897b5de17 100644
--- a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb
@@ -31,6 +31,7 @@ builddependencies = [
     ('gettext', '0.20.1'),
     ('pkg-config', '0.29.2'),
     ('intltool', '0.51.0'),
+    ('Doxygen', '1.8.16'),
 ]
 
 default_easyblock = 'ConfigureMake'
diff --git a/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb
index 0c4398adb92..ae81bf67362 100644
--- a/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb
@@ -26,6 +26,7 @@ builddependencies = [
     ('intltool', '0.51.0'),
     ('Meson', '0.55.1', '-Python-3.8.2'),
     ('Ninja', '1.10.0'),
+    ('Doxygen', '1.8.17'),
 ]
 dependencies = [
     ('bzip2', '1.0.8'),
diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb
index d1a9f51ec07..c5a69cfdb84 100644
--- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb
@@ -26,6 +26,7 @@ builddependencies = [
     ('intltool', '0.51.0'),
     ('Meson', '0.55.3'),
     ('Ninja', '1.10.1'),
+    ('Doxygen', '1.8.20'),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb
index b2104033854..e277989781e 100644
--- a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb
@@ -26,6 +26,7 @@ builddependencies = [
     ('intltool', '0.51.0'),
     ('Meson', '0.58.0'),
     ('Ninja', '1.10.2'),
+    ('Doxygen', '1.9.1'),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb
index 259c0017c55..adc8a9e814b 100644
--- a/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb
@@ -26,6 +26,7 @@ builddependencies = [
     ('intltool', '0.51.0'),
     ('Meson', '0.58.2'),
     ('Ninja', '1.10.2'),
+    ('Doxygen', '1.9.1'),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb
index d417d954c4b..0b3c1e7407b 100644
--- a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb
@@ -26,6 +26,7 @@ builddependencies = [
     ('intltool', '0.51.0'),
     ('Meson', '0.62.1'),
     ('Ninja', '1.10.2'),
+    ('Doxygen', '1.9.4'),
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb
index ea22050d122..f98e6b15dbc 100644
--- a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb
@@ -26,6 +26,7 @@ builddependencies = [
     ('intltool', '0.51.0'),
     ('Meson', '0.64.0'),
     ('Ninja', '1.11.1'),
+    ('Doxygen', '1.9.5'),
 ]
 
 dependencies = [

From c21337d03bda7d5be2098ecd774bb5ec3c97c732 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 2 May 2023 13:31:32 +0200
Subject: [PATCH 462/601] adding easyconfigs: Rtree-1.0.1-GCCcore-12.2.0.eb,
 libspatialindex-1.9.3-GCCcore-12.2.0.eb

---
 .../libspatialindex-1.9.3-GCCcore-12.2.0.eb   | 25 +++++++++++++++++
 .../r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb     | 28 +++++++++++++++++++
 2 files changed, 53 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..0535f0e96f8
--- /dev/null
+++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'CMakeMake'
+
+name = 'libspatialindex'
+version = '1.9.3'
+
+homepage = 'https://libspatialindex.org'
+description = """C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/libspatialindex/libspatialindex/releases/download/%(version)s/']
+sources = ['spatialindex-src-%(version)s.tar.gz']
+checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libspatialindex.%s' % SHLIB_EXT],
+    'dirs': ['include/spatialindex'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..5650717ef68
--- /dev/null
+++ b/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'PythonPackage'
+
+name = 'Rtree'
+version = '1.0.1'
+
+homepage = 'https://toblerity.org/rtree/'
+description = """Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial
+ indexing features for the spatially curious Python user."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['222121699c303a64065d849bf7038b1ecabc37b65c7fa340bedb38ef0e805429']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('libspatialindex', '1.9.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+moduleclass = 'data'

From cb4bd2fd96026b32434cd910050025413c5527e8 Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 2 May 2023 14:49:08 +0200
Subject: [PATCH 463/601] adding easyconfigs: xxHash-0.8.1-GCCcore-12.2.0.eb,
 python-xxhash-3.2.0-GCCcore-12.2.0.eb

---
 .../python-xxhash-3.2.0-GCCcore-12.2.0.eb     | 29 +++++++++++++++++
 .../x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb   | 31 +++++++++++++++++++
 2 files changed, 60 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..54e733c36c8
--- /dev/null
+++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonBundle'
+
+name = 'python-xxhash'
+version = '3.2.0'
+
+homepage = 'https://github.com/ifduyue/python-xxhash'
+description = 'xxhash is a Python binding for the xxHash library by Yann Collet.'
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('xxHash', '0.8.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('xxhash', version, {
+        'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'],
+    }),
+]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..1cb665e6061
--- /dev/null
+++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'xxHash'
+version = '0.8.1'
+
+homepage = 'https://cyan4973.github.io/xxHash'
+description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['3bb6b7d6f30c591dd65aaaff1c8b7a5b94d81687998ca9400082c739a690436c']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+skipsteps = ['configure']
+
+installopts = "PREFIX=%(installdir)s"
+
+sanity_check_paths = {
+    'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h',
+              'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'],
+    'dirs': ['share/man'],
+}
+
+sanity_check_commands = ["xxhsum --help"]
+
+moduleclass = 'tools'

From 79b0363bd7b281997d672d23dbf9503312dbc9ee Mon Sep 17 00:00:00 2001
From: Simon Pinches <Simon.Pinches@iter.org>
Date: Tue, 2 May 2023 17:25:20 +0200
Subject: [PATCH 464/601] adding easyconfigs: Pandoc-3.1.2.eb

---
 .../easyconfigs/p/Pandoc/Pandoc-3.1.2.eb      | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb

diff --git a/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb
new file mode 100644
index 00000000000..5916797cde8
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb
@@ -0,0 +1,32 @@
+# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+# Contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'Tarball'
+
+name = 'Pandoc'
+version = '3.1.2'
+
+homepage = 'https://pandoc.org'
+description = "If you need to convert files from one markup format into another, pandoc is your swiss-army knife"
+
+toolchain = SYSTEM
+
+_archs = {'x86_64': 'amd64', 'aarch64': 'arm64'}
+
+source_urls = ['https://github.com/jgm/pandoc/releases/download/%(version)s/']
+sources = ['%%(namelower)s-%%(version)s-linux-%s.tar.gz' % _archs[ARCH]]
+checksums = ['4e1c607f7e4e9243fa1e1f5b208cd4f1d3f6fd055d5d8c39ba0cdc38644e1c35']
+
+sanity_check_paths = {
+    'files': ['bin/pandoc'],
+    'dirs': ['share'],
+}
+
+sanity_check_commands = ['pandoc --help']
+
+moduleclass = 'tools'

From c5dd2aab92a81d29afbafa87dcde688e240e210a Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 3 May 2023 12:01:44 +0100
Subject: [PATCH 465/601] adding easyconfigs: Gurobi-10.0.1-GCCcore-12.2.0.eb

---
 .../g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb  | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..7f8752b1f3f
--- /dev/null
+++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb
@@ -0,0 +1,39 @@
+name = 'Gurobi'
+version = '10.0.1'
+
+homepage = 'https://www.gurobi.com'
+description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming.
+The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern
+architectures and multi-core processors, using the most advanced implementations of the
+latest algorithms."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/']
+sources = ['%(namelower)s%(version)s_linux64.tar.gz']
+patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch']
+checksums = [
+    {'gurobi10.0.1_linux64.tar.gz': 'a0b551156df2c94107b3428cae278716a0a6c913f63ac132573852b9725b6c59'},
+    {'Gurobi-9.0.1_use-eb-python-gurobi-shell.patch':
+     'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01'},
+]
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
+dependencies = [
+    ('Python', '3.10.8'),
+]
+
+# remove bundled Python interpreter in favour of the dependency in EB
+postinstallcmds = ['rm %(installdir)s/bin/python*']
+
+# license is mandatory for installation
+license_file = "HOME" + '/licenses/%(name)s.lic'
+
+modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh`
+Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy'
+"""
+
+moduleclass = 'math'

From 9f297980819762b7a4fd5671b811b94986ba6777 Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Wed, 3 May 2023 13:42:15 +0200
Subject: [PATCH 466/601] adding easyconfigs: CPC2-0.1-foss-2022a.eb and
 patches: CPC2-0.1_fix_libsvm_path_and_python2.patch

---
 .../easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 40 +++++++++
 ...CPC2-0.1_fix_libsvm_path_and_python2.patch | 82 +++++++++++++++++++
 2 files changed, 122 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
new file mode 100644
index 00000000000..59ab7d33d1f
--- /dev/null
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
@@ -0,0 +1,40 @@
+# Author: Samuel Moors, Vrije Universiteit Brussel (VUB)
+# Updated: Denis Kristak (Inuits)
+# Update to a Python3 version
+easyblock = 'PackedBinary'
+
+name = 'CPC2'
+version = '0.1'
+local_commit = '813487e'
+
+homepage = 'http://cpc2.cbi.pku.edu.cn'
+description = """ a fast and accurate coding potential calculator based on sequence intrinsic features  """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available
+# download from github mirror
+source_urls = ['https://github.com/lucventurini/CPC2/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+patches = ['%(name)s-%(version)s_fix_libsvm_path_and_python2.patch']
+checksums = [
+    {'CPC2-0.1.tar.gz': '6fd4f3fb05b179073709c033481ae082085eabc7c5281cd743c9419d3ec6de67'},
+    {'CPC2-0.1_fix_libsvm_path_and_python2.patch': '657f552ebfad925e8c051a19426cd5bb1b8ad7da8cdcc3e701e1220673330842'},
+]
+
+dependencies = [ 
+    ('Python', '3.10.4'),
+    ('LIBSVM', '3.30'),
+    ('Biopython', '1.79'),
+]
+
+install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/'
+
+sanity_check_paths = { 
+    'files': ['bin/CPC2.py'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch b/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch
new file mode 100644
index 00000000000..38190f1c201
--- /dev/null
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch
@@ -0,0 +1,82 @@
+Use libsvm from the environment instead of the one provided with CPC2
+Author: Samuel Moors, Vrije Universiteit Brussel (VUB)
+Update: Fix incompatible syntax with Python 3
+Updated by: Denis Kristak (Inuits)
+diff -ruN cpc2_orig/bin/compress.py cpc2/bin/compress.py
+--- cpc2_orig/bin/compress.py	2018-10-22 17:58:22.000000000 +0200
++++ cpc2/bin/compress.py	2023-05-03 12:37:36.240001307 +0200
+@@ -11,7 +11,7 @@
+ 			fq_fp = gzip.open(fq_file,mode+"b",level)
+ 		else:
+ 			sys.stderr.write("[INFO] read file '%s'\n"%fq_file)
+-			fq_fp = file(fq_file,mode)
++			fq_fp = open(fq_file,mode)
+ 	except:
+ 		sys.stderr.write("Error: Fail to IO file: %s\n"%(fq_file))
+ 		sys.exit(1)
+diff -ruN cpc2_orig/bin/CPC2.py cpc2/bin/CPC2.py
+--- cpc2_orig/bin/CPC2.py	2023-05-02 16:41:34.222887000 +0200
++++ cpc2/bin/CPC2.py	2023-05-03 12:40:15.817915000 +0200
+@@ -78,7 +78,7 @@
+ 		'''
+ 		while True:
+ 			try: 
+-				codon,index = triplet_got.next()
++				codon,index = next(triplet_got)
+ 			except StopIteration:
+ 				break 
+ 			if codon in starts and codon not in stops:
+@@ -89,7 +89,7 @@
+ 				end_extension = False
+ 				while True:
+ 					try: 
+-						codon,index = triplet_got.next()
++						codon,index = next(triplet_got)
+ 					except StopIteration:
+ 						end_extension = True
+ 						integrity = -1
+@@ -245,9 +245,9 @@
+ 	'''
+ 	strinfoAmbiguous = re.compile("X|B|Z|J|U",re.I)
+ 	ptU = re.compile("U",re.I)
+-	ftmp_feat = file(outfile + ".feat","w")
+-	ftmp_svm = file(outfile + ".tmp.1","w")
+-	ftmp_result = file(outfile,"w")
++	ftmp_feat = open(outfile + ".feat","w")
++	ftmp_svm = open(outfile + ".tmp.1","w")
++	ftmp_result = open(outfile,"w")
+ 	ftmp_result.write("\t".join(map(str,["#ID","transcript_length","peptide_length","Fickett_score","pI","ORF_integrity","coding_probability","label"]))+"\n")
+ 	ftmp_result.close()
+ 	fickett_obj = Fickett()
+@@ -288,16 +288,16 @@
+ 	script_dir,filename = os.path.split(os.path.abspath(sys.argv[0]))
+ 	data_dir = script_dir + "/../data/"
+ 	lib_dir = script_dir + "/../libs/"
+-	app_svm_scale = lib_dir + "libsvm/libsvm-3.18/svm-scale"
+-	app_svm_predict = lib_dir + "libsvm/libsvm-3.18/svm-predict"
+-	os.system('test -x '+ app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr')
+-	os.system('test -x '+ app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr')
++	app_svm_scale = 'svm-scale'
++	app_svm_predict = 'svm-predict'
++	os.system('which ' + app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr')
++	os.system('which ' + app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr')
+ 	
+ 	cmd = app_svm_scale + ' -r ' + data_dir + 'cpc2.range ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&'
+ 	cmd = cmd + app_svm_predict + ' -b 1 -q ' + outfile + '.tmp.2 ' + data_dir + 'cpc2.model ' + outfile + '.tmp.1 &&'
+ 	cmd = cmd + 'awk -vOFS="\\t" \'{if ($1 == 1){print $2,"coding"} else if ($1 == 0){print $2,"noncoding"}}\' ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&'
+ 	cmd = cmd + 'paste ' + outfile + '.feat ' + outfile + '.tmp.2 >>' + outfile
+-	command = suprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
++	command = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ 	(outtext, errtext) = command.communicate()
+ 	exitstatus = command.returncode
+ 	os.system('rm -f ' + outfile + '.tmp.1 ' + outfile + '.tmp.2')
+@@ -306,7 +306,8 @@
+ 	#	pass
+ 	if exitstatus == 0:
+ 		rm_cmd = "rm -f " + outfile + '.feat'
+-		subprocess.call(rm_cmd)
++		print(rm_cmd)
++		subprocess.run(rm_cmd, shell=True)
+ 		sys.stderr.write("[INFO] Running Done!\n")
+ 		return 0
+ 	else:

From 7d9fcc0bd7a218ce8e41aa29db6f93287c6756b5 Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Wed, 3 May 2023 13:57:42 +0200
Subject: [PATCH 467/601] code style

---
 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
index 59ab7d33d1f..043d64d9573 100644
--- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
@@ -22,7 +22,7 @@ checksums = [
     {'CPC2-0.1_fix_libsvm_path_and_python2.patch': '657f552ebfad925e8c051a19426cd5bb1b8ad7da8cdcc3e701e1220673330842'},
 ]
 
-dependencies = [ 
+dependencies = [
     ('Python', '3.10.4'),
     ('LIBSVM', '3.30'),
     ('Biopython', '1.79'),
@@ -30,7 +30,7 @@ dependencies = [
 
 install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/'
 
-sanity_check_paths = { 
+sanity_check_paths = {
     'files': ['bin/CPC2.py'],
     'dirs': [],
 }

From 602e7cf7cc55bad3ff70b11544290dee5fbe81a1 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 3 May 2023 14:39:14 +0200
Subject: [PATCH 468/601] adding easyconfigs: SoupX-1.6.2-foss-2022a-R-4.2.1.eb

---
 .../s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..3354780d23e
--- /dev/null
+++ b/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,29 @@
+easyblock = 'RPackage'
+
+name = 'SoupX'
+version = '1.6.2'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/constantAmateur/SoupX'
+description = """"
+Quantify, profile and remove ambient mRNA contamination (the "soup") from
+droplet based single cell RNA-seq experiments. Implements the method described
+in Young et al. (2018) <doi:10.1101/303727>."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://cran.r-project.org/src/contrib/']
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['9b6226cd7c0691498a874d5c029f8ff81fd2060295c298985397521c1f7ee3a5']
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('Seurat', '4.3.0', versionsuffix)
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+moduleclass = 'bio'

From 7877a55877e5c9ad47d9ff3fd6df6cdeda7e31a1 Mon Sep 17 00:00:00 2001
From: Neil Douglas <neil.douglas@york.ac.uk>
Date: Wed, 3 May 2023 14:17:05 +0100
Subject: [PATCH 469/601] Add exts epitools to R-4.2.1 & deepSNV to
 R-bundle-Bioconductor

---
 ...bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 15 +++++++++++----
 easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb   |  3 +++
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
index 72d0887ac92..c6c39172ea7 100644
--- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
+++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
@@ -11,7 +11,8 @@ description = """Bioconductor provides tools for the analysis and coprehension
 toolchain = {'name': 'foss', 'version': '2022a'}
 
 # lpsymphony fails to build with pkgconf, so stick to pkg-config
-# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286
+# error in:
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286
 builddependencies = [('pkg-config', '0.29.2')]
 
 dependencies = [
@@ -28,9 +29,11 @@ exts_default_options = {
         'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s',
         'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/',
         'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/',
-        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        # package archive
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',
         'https://cran.r-project.org/src/contrib/',  # current version of packages
-        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+        # mirror alternative for current packages
+        'https://cran.freestatistics.org/src/contrib',
     ],
     'source_tmpl': '%(name)s_%(version)s.tar.gz'
 }
@@ -41,7 +44,8 @@ exts_defaultclass = 'RPackage'
 # (some versions in this bundle may be newer than the ones provided by R)
 local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') "
 local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')"
-exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg))
+exts_filter = ("R -q --no-save", "%s { %s }" %
+               (local_ext_version_check, local_stop_msg))
 
 # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends
 # !! order of packages is important !!
@@ -1206,6 +1210,9 @@ exts_list = [
     ('SpatialExperiment', '1.6.1', {
         'checksums': ['31e516e14e827e4b9fe853bc136066863dd762053012631c569ec3c00c6cbab5'],
     }),
+    ('deepSNV', '1.42.1', {
+        'checksums': ['f64d43645d696af7b375c66f7dccf877d099482f8470dd18c4aba8b1f30bf22d'],
+    }),
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}
diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
index c0a40a9552d..313583b74ab 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb
@@ -3523,6 +3523,9 @@ exts_list = [
     ('word2vec', '0.3.4', {
         'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'],
     }),
+    ('epitools', '0.5-10.1', {
+        'checksums': ['b418854de1fcedd126f3bf19dc27e8a71ee6efae5371098ab64a53a2d51d164b'],
+    }),
 ]
 
 moduleclass = 'lang'

From 412b0d96c4b77b6531a71f5188c9e4ccd91037ee Mon Sep 17 00:00:00 2001
From: Neil Douglas <neil.douglas@york.ac.uk>
Date: Wed, 3 May 2023 14:24:47 +0100
Subject: [PATCH 470/601] Formatting

---
 .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
index c6c39172ea7..d19d5c0d3c5 100644
--- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
+++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
@@ -11,8 +11,7 @@ description = """Bioconductor provides tools for the analysis and coprehension
 toolchain = {'name': 'foss', 'version': '2022a'}
 
 # lpsymphony fails to build with pkgconf, so stick to pkg-config
-# error in:
-# https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286
+# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286
 builddependencies = [('pkg-config', '0.29.2')]
 
 dependencies = [
@@ -28,12 +27,10 @@ exts_default_options = {
         'https://bioconductor.org/packages/3.15/bioc/src/contrib/',
         'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s',
         'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/',
-        'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/',
-        # package archive
+        'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/',  # package archive
         'https://cran.r-project.org/src/contrib/Archive/%(name)s',
         'https://cran.r-project.org/src/contrib/',  # current version of packages
-        # mirror alternative for current packages
-        'https://cran.freestatistics.org/src/contrib',
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
     ],
     'source_tmpl': '%(name)s_%(version)s.tar.gz'
 }
@@ -44,8 +41,7 @@ exts_defaultclass = 'RPackage'
 # (some versions in this bundle may be newer than the ones provided by R)
 local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') "
 local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')"
-exts_filter = ("R -q --no-save", "%s { %s }" %
-               (local_ext_version_check, local_stop_msg))
+exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg))
 
 # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends
 # !! order of packages is important !!

From 880eba1cfb0cbc2806ac121abd21dea4e6862d93 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 3 May 2023 14:25:10 +0100
Subject: [PATCH 471/601] adding easyconfigs: Pyomo-6.5.0-foss-2022b.eb

---
 .../p/Pyomo/Pyomo-6.5.0-foss-2022b.eb         | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb
new file mode 100644
index 00000000000..8e787b4623c
--- /dev/null
+++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb
@@ -0,0 +1,32 @@
+easyblock = 'PythonBundle'
+
+name = 'Pyomo'
+version = '6.5.0'
+
+homepage = 'https://www.pyomo.org/'
+description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization
+ capabilities for formulating and analyzing optimization models. """
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [('Python', '3.10.8')]
+
+exts_list = [
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('PyUtilib', '6.0.0', {
+        'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'],
+        'preinstallopts': """sed -i "s/'nose',//g" setup.py && """,
+    }),
+    (name, version, {
+        'checksums': ['5a23e775bba9fdbad22698fa1a841e662482edc979f2dea41cc6c54b1bb4b968'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_commands = ['pyomo -h']
+
+moduleclass = 'math'

From 2224e67bbeb0c4ef66bcb8f64d67be0b980d2048 Mon Sep 17 00:00:00 2001
From: Neil Douglas <neil.douglas@york.ac.uk>
Date: Wed, 3 May 2023 14:27:31 +0100
Subject: [PATCH 472/601] Replace comment

---
 .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
index d19d5c0d3c5..1ccecc5efcd 100644
--- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
+++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb
@@ -27,8 +27,8 @@ exts_default_options = {
         'https://bioconductor.org/packages/3.15/bioc/src/contrib/',
         'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s',
         'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/',
-        'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/',  # package archive
-        'https://cran.r-project.org/src/contrib/Archive/%(name)s',
+        'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/',
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
         'https://cran.r-project.org/src/contrib/',  # current version of packages
         'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
     ],

From 3b3790756bc2dc37b65444bb3f8eb98cde0ba268 Mon Sep 17 00:00:00 2001
From: sassy <sassy@hp>
Date: Wed, 3 May 2023 16:18:12 +0100
Subject: [PATCH 473/601] Missing mpi4py added

---
 easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb
index 8e787b4623c..c924968a115 100644
--- a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb
@@ -9,7 +9,10 @@ description = """ Pyomo is a Python-based open-source software package that supp
 
 toolchain = {'name': 'foss', 'version': '2022b'}
 
-dependencies = [('Python', '3.10.8')]
+dependencies = [
+    ('Python', '3.10.8'),
+    ('mpi4py', '3.1.4'),
+]
 
 exts_list = [
     ('ply', '3.11', {

From 28b35d2903b221d915a5bf7fbca40f982474bbd0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 May 2023 11:53:12 +0200
Subject: [PATCH 474/601] also check for 'data' in sanity check for CPC2

---
 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
index 043d64d9573..9bcd7cf4116 100644
--- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
@@ -32,7 +32,7 @@ install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/'
 
 sanity_check_paths = {
     'files': ['bin/CPC2.py'],
-    'dirs': [],
+    'dirs': ['data'],
 }
 
 sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out']

From a3bcf2047353256ac1d3048762e8d9d1fb33b850 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Thu, 4 May 2023 13:53:24 +0200
Subject: [PATCH 475/601] adding easyconfigs:
 CellChat-1.5.0-foss-2022a-R-4.2.1.eb

---
 .../CellChat-1.5.0-foss-2022a-R-4.2.1.eb      | 57 +++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..97b28ca1651
--- /dev/null
+++ b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,57 @@
+easyblock = 'Bundle'
+
+name = 'CellChat'
+version = '1.5.0'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://github.com/sqjin/CellChat'
+description = """"
+R toolkit for inference, visualization and analysis of cell-cell communication
+from single-cell data"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('R-bundle-Bioconductor', '3.15', versionsuffix),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('umap-learn', '0.5.3'),
+]
+
+exts_defaultclass = 'RPackage'
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
+
+exts_list = [
+    ('ggalluvial', '0.12.5', {
+        'checksums': ['90044c880e70096137a733d601b11e558fe55e4e7d3aaacac6f08d7847415d71'],
+    }),
+    ('systemfonts', '1.0.4', {
+        'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'],
+    }),
+    ('svglite', '2.1.1', {
+        'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'],
+    }),
+    (name, version, {
+        'preinstallopts': "rm src/*.o src/*.so && ",
+        'source_urls': ['https://github.com/sqjin/CellChat/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['c9e31327cbbcf1fec5e6d8a0dfe011ded8e543557107e93dd4a417c4c137d1c6'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'bio'

From e18a0cc06d871e622a373946a5ec22b51c2d0f5b Mon Sep 17 00:00:00 2001
From: Jasper <65227842+jfgrimm@users.noreply.github.com>
Date: Thu, 4 May 2023 14:18:08 +0100
Subject: [PATCH 476/601] comment license

---
 .../easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb      | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb
index 7f8752b1f3f..4eeb0dae621 100644
--- a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb
@@ -30,7 +30,9 @@ dependencies = [
 postinstallcmds = ['rm %(installdir)s/bin/python*']
 
 # license is mandatory for installation
-license_file = "HOME" + '/licenses/%(name)s.lic'
+# use EB_GUROBI_LICENSE_FILE environment variable, or 
+# uncomment and modify the following variable:
+# license_file = '/path/to/my-license-file'
 
 modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh`
 Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy'

From 6e32e71b8b50058388165704a3088ab5325249cc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 May 2023 17:09:33 +0200
Subject: [PATCH 477/601] adding easyconfigs: rustworkx-0.12.1-foss-2022a.eb

---
 .../rustworkx/rustworkx-0.12.1-foss-2022a.eb  | 169 ++++++++++++++++++
 1 file changed, 169 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb
new file mode 100644
index 00000000000..73bcca7c937
--- /dev/null
+++ b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb
@@ -0,0 +1,169 @@
+easyblock = "CargoPythonPackage"
+
+name = 'rustworkx'
+version = '0.12.1'
+
+homepage = 'https://github.com/Qiskit/rustworkx'
+description = """rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take
+advantage of the performance and safety that Rust provides. It is designed to provide a high performance general
+purpose graph library for any Python application."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('Rust', '1.65.0'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+]
+
+crates = [
+    ('ahash', '0.7.6'),
+    ('autocfg', '1.1.0'),
+    ('bitflags', '1.3.2'),
+    ('cfg-if', '1.0.0'),
+    ('crossbeam-channel', '0.5.4'),
+    ('crossbeam-deque', '0.8.1'),
+    ('crossbeam-epoch', '0.9.8'),
+    ('crossbeam-utils', '0.8.8'),
+    ('either', '1.6.1'),
+    ('fixedbitset', '0.4.2'),
+    ('getrandom', '0.2.6'),
+    ('hashbrown', '0.11.2'),
+    ('hermit-abi', '0.1.19'),
+    ('indexmap', '1.7.0'),
+    ('indoc', '1.0.6'),
+    ('instant', '0.1.12'),
+    ('itoa', '1.0.2'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.126'),
+    ('lock_api', '0.4.7'),
+    ('matrixmultiply', '0.2.4'),
+    ('memchr', '2.5.0'),
+    ('memoffset', '0.6.5'),
+    ('ndarray', '0.13.1'),
+    ('num-bigint', '0.4.3'),
+    ('num-complex', '0.2.4'),
+    ('num-complex', '0.4.1'),
+    ('num-integer', '0.1.45'),
+    ('num-traits', '0.2.15'),
+    ('num_cpus', '1.13.1'),
+    ('numpy', '0.17.2'),
+    ('once_cell', '1.12.0'),
+    ('parking_lot', '0.11.2'),
+    ('parking_lot_core', '0.8.5'),
+    ('petgraph', '0.6.2'),
+    ('ppv-lite86', '0.2.16'),
+    ('priority-queue', '1.2.0'),
+    ('proc-macro2', '1.0.39'),
+    ('pyo3', '0.17.3'),
+    ('pyo3-build-config', '0.17.3'),
+    ('pyo3-ffi', '0.17.3'),
+    ('pyo3-macros', '0.17.3'),
+    ('pyo3-macros-backend', '0.17.3'),
+    ('quick-xml', '0.22.0'),
+    ('quote', '1.0.18'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.6.3'),
+    ('rand_pcg', '0.3.1'),
+    ('rawpointer', '0.2.1'),
+    ('rayon', '1.5.3'),
+    ('rayon-core', '1.9.3'),
+    ('redox_syscall', '0.2.13'),
+    ('ryu', '1.0.10'),
+    ('scopeguard', '1.1.0'),
+    ('serde', '1.0.145'),
+    ('serde_derive', '1.0.145'),
+    ('serde_json', '1.0.89'),
+    ('smallvec', '1.8.0'),
+    ('syn', '1.0.96'),
+    ('target-lexicon', '0.12.4'),
+    ('unicode-ident', '1.0.0'),
+    ('unindent', '0.1.9'),
+    ('version_check', '0.9.4'),
+    ('wasi', '0.10.2+wasi-snapshot-preview1'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = [
+    {'rustworkx-0.12.1.tar.gz': '13a19a2f64dff086b3bffffb294c4630100ecbc13634b4995d9d36a481ae130e'},
+    {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'},
+    {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'crossbeam-channel-0.5.4.tar.gz': '5aaa7bd5fb665c6864b5f963dd9097905c54125909c7aa94c9e18507cdbe6c53'},
+    {'crossbeam-deque-0.8.1.tar.gz': '6455c0ca19f0d2fbf751b908d5c55c1f5cbc65e03c4225427254b46890bdde1e'},
+    {'crossbeam-epoch-0.9.8.tar.gz': '1145cf131a2c6ba0615079ab6a638f7e1973ac9c2634fcbeaaad6114246efe8c'},
+    {'crossbeam-utils-0.8.8.tar.gz': '0bf124c720b7686e3c2663cf54062ab0f68a88af2fb6a030e87e30bf721fcb38'},
+    {'either-1.6.1.tar.gz': 'e78d4f1cc4ae33bbfc157ed5d5a5ef3bc29227303d595861deb238fcec4e9457'},
+    {'fixedbitset-0.4.2.tar.gz': '0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80'},
+    {'getrandom-0.2.6.tar.gz': '9be70c98951c83b8d2f8f60d7065fa6d5146873094452a1008da8c2f1e4205ad'},
+    {'hashbrown-0.11.2.tar.gz': 'ab5ef0d4909ef3724cc8cce6ccc8572c5c817592e9285f5464f8e86f8bd3726e'},
+    {'hermit-abi-0.1.19.tar.gz': '62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33'},
+    {'indexmap-1.7.0.tar.gz': 'bc633605454125dec4b66843673f01c7df2b89479b32e0ed634e43a91cff62a5'},
+    {'indoc-1.0.6.tar.gz': '05a0bd019339e5d968b37855180087b7b9d512c5046fbd244cf8c95687927d6e'},
+    {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'},
+    {'itoa-1.0.2.tar.gz': '112c678d4050afce233f4f2852bb2eb519230b3cf12f33585275537d7e41578d'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'libc-0.2.126.tar.gz': '349d5a591cd28b49e1d1037471617a32ddcda5731b99419008085f72d5a53836'},
+    {'lock_api-0.4.7.tar.gz': '327fa5b6a6940e4699ec49a9beae1ea4845c6bab9314e4f84ac68742139d8c53'},
+    {'matrixmultiply-0.2.4.tar.gz': '916806ba0031cd542105d916a97c8572e1fa6dd79c9c51e7eb43a09ec2dd84c1'},
+    {'memchr-2.5.0.tar.gz': '2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d'},
+    {'memoffset-0.6.5.tar.gz': '5aa361d4faea93603064a027415f07bd8e1d5c88c9fbf68bf56a285428fd79ce'},
+    {'ndarray-0.13.1.tar.gz': 'ac06db03ec2f46ee0ecdca1a1c34a99c0d188a0d83439b84bf0cb4b386e4ab09'},
+    {'num-bigint-0.4.3.tar.gz': 'f93ab6289c7b344a8a9f60f88d80aa20032336fe78da341afc91c8a2341fc75f'},
+    {'num-complex-0.2.4.tar.gz': 'b6b19411a9719e753aff12e5187b74d60d3dc449ec3f4dc21e3989c3f554bc95'},
+    {'num-complex-0.4.1.tar.gz': '97fbc387afefefd5e9e39493299f3069e14a140dd34dc19b4c1c1a8fddb6a790'},
+    {'num-integer-0.1.45.tar.gz': '225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9'},
+    {'num-traits-0.2.15.tar.gz': '578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd'},
+    {'num_cpus-1.13.1.tar.gz': '19e64526ebdee182341572e50e9ad03965aa510cd94427a4549448f285e957a1'},
+    {'numpy-0.17.2.tar.gz': 'a462c1af5ba1fddec1488c4646993a23ae7931f9e170ccba23e9c7c834277797'},
+    {'once_cell-1.12.0.tar.gz': '7709cef83f0c1f58f666e746a08b21e0085f7440fa6a29cc194d68aac97a4225'},
+    {'parking_lot-0.11.2.tar.gz': '7d17b78036a60663b797adeaee46f5c9dfebb86948d1255007a1d6be0271ff99'},
+    {'parking_lot_core-0.8.5.tar.gz': 'd76e8e1493bcac0d2766c42737f34458f1c8c50c0d23bcb24ea953affb273216'},
+    {'petgraph-0.6.2.tar.gz': 'e6d5014253a1331579ce62aa67443b4a658c5e7dd03d4bc6d302b94474888143'},
+    {'ppv-lite86-0.2.16.tar.gz': 'eb9f9e6e233e5c4a35559a617bf40a4ec447db2e84c20b55a6f83167b7e57872'},
+    {'priority-queue-1.2.0.tar.gz': 'cf40e51ccefb72d42720609e1d3c518de8b5800d723a09358d4a6d6245e1f8ca'},
+    {'proc-macro2-1.0.39.tar.gz': 'c54b25569025b7fc9651de43004ae593a75ad88543b17178aa5e1b9c4f15f56f'},
+    {'pyo3-0.17.3.tar.gz': '268be0c73583c183f2b14052337465768c07726936a260f480f0857cb95ba543'},
+    {'pyo3-build-config-0.17.3.tar.gz': '28fcd1e73f06ec85bf3280c48c67e731d8290ad3d730f8be9dc07946923005c8'},
+    {'pyo3-ffi-0.17.3.tar.gz': '0f6cb136e222e49115b3c51c32792886defbfb0adead26a688142b346a0b9ffc'},
+    {'pyo3-macros-0.17.3.tar.gz': '94144a1266e236b1c932682136dc35a9dee8d3589728f68130c7c3861ef96b28'},
+    {'pyo3-macros-backend-0.17.3.tar.gz': 'c8df9be978a2d2f0cdebabb03206ed73b11314701a5bfe71b0d753b81997777f'},
+    {'quick-xml-0.22.0.tar.gz': '8533f14c8382aaad0d592c812ac3b826162128b65662331e1127b45c3d18536b'},
+    {'quote-1.0.18.tar.gz': 'a1feb54ed693b93a84e14094943b84b7c4eae204c512b7ccb95ab0c66d278ad1'},
+    {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'},
+    {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'},
+    {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'},
+    {'rand_pcg-0.3.1.tar.gz': '59cad018caf63deb318e5a4586d99a24424a364f40f1e5778c29aca23f4fc73e'},
+    {'rawpointer-0.2.1.tar.gz': '60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3'},
+    {'rayon-1.5.3.tar.gz': 'bd99e5772ead8baa5215278c9b15bf92087709e9c1b2d1f97cdb5a183c933a7d'},
+    {'rayon-core-1.9.3.tar.gz': '258bcdb5ac6dad48491bb2992db6b7cf74878b0384908af124823d118c99683f'},
+    {'redox_syscall-0.2.13.tar.gz': '62f25bc4c7e55e0b0b7a1d43fb893f4fa1361d0abe38b9ce4f323c2adfe6ef42'},
+    {'ryu-1.0.10.tar.gz': 'f3f6f92acf49d1b98f7a81226834412ada05458b7364277387724a237f062695'},
+    {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'},
+    {'serde-1.0.145.tar.gz': '728eb6351430bccb993660dfffc5a72f91ccc1295abaa8ce19b27ebe4f75568b'},
+    {'serde_derive-1.0.145.tar.gz': '81fa1584d3d1bcacd84c277a0dfe21f5b0f6accf4a23d04d4c6d61f1af522b4c'},
+    {'serde_json-1.0.89.tar.gz': '020ff22c755c2ed3f8cf162dbb41a7268d934702f3ed3631656ea597e08fc3db'},
+    {'smallvec-1.8.0.tar.gz': 'f2dd574626839106c320a323308629dcb1acfc96e32a8cba364ddc61ac23ee83'},
+    {'syn-1.0.96.tar.gz': '0748dd251e24453cb8717f0354206b91557e4ec8703673a4b30208f2abaf1ebf'},
+    {'target-lexicon-0.12.4.tar.gz': 'c02424087780c9b71cc96799eaeddff35af2bc513278cda5c99fc1f5d026d3c1'},
+    {'unicode-ident-1.0.0.tar.gz': 'd22af068fba1eb5edcb4aea19d382b2a3deb4c8f9d475c589b6ada9e0fd493ee'},
+    {'unindent-0.1.9.tar.gz': '52fee519a3e570f7df377a06a1a7775cdbfb7aa460be7e08de2b1f0e69973a44'},
+    {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'},
+    {'wasi-0.10.2+wasi-snapshot-preview1.tar.gz': 'fd6fbd9a79829dd1ad0cc20627bf1ed606756a7f77edff7b66b7064f9cb327c6'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'math'

From 4730edaa631fe8db8d00c5a0fc1d5bd5dabea3d9 Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Thu, 4 May 2023 18:29:36 +0200
Subject: [PATCH 478/601] adding easyconfigs: Zip-3.0-GCCcore-12.2.0.eb

---
 .../z/Zip/Zip-3.0-GCCcore-12.2.0.eb           | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..84708515be8
--- /dev/null
+++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'ConfigureMake'
+
+name = 'Zip'
+version = '3.0'
+
+homepage = 'http://www.info-zip.org/Zip.html'
+description = """Zip is a compression and file packaging/archive utility.
+Although highly compatible both with PKWARE's PKZIP and PKUNZIP
+utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives
+have been portability and other-than-MSDOS functionality"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://download.sourceforge.net/infozip']
+sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz']
+checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369']
+
+builddependencies = [
+    ('binutils', '2.39'),
+]
+dependencies = [
+    ('bzip2', '1.0.8'),
+]
+
+skipsteps = ['configure']
+
+buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 '
+buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" '
+buildopts += 'generic_gcc'
+
+installopts = '-f unix/Makefile prefix=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'],
+    'dirs': ['man/man1']
+}
+
+sanity_check_commands = ["zip --version"]
+
+moduleclass = 'tools'

From d8abe94bcc09f3b35095c61e423f0f5ae04940ce Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Thu, 4 May 2023 18:36:15 +0200
Subject: [PATCH 479/601] adding easyconfigs:
 Abseil-20230125.2-GCCcore-12.2.0.eb

---
 .../Abseil-20230125.2-GCCcore-12.2.0.eb       | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..ac3526452ed
--- /dev/null
+++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'Abseil'
+version = '20230125.2'
+
+homepage = 'https://abseil.io/'
+description = """Abseil is an open-source collection of C++ library code designed to augment the
+C++ standard library. The Abseil library code is collected from Google's own
+C++ code base, has been extensively tested and used in production, and is the
+same code we depend on in our daily coding lives."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++17'}
+
+source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags']
+sources = ['%(version)s.tar.gz']
+checksums = ['9a2b5752d7bfade0bdeee2701de17c9480620f8b237e1964c1b9967c75374906']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+
+sanity_check_paths = {
+    'files': ['lib/libabsl_base.%s' % SHLIB_EXT],
+    'dirs': ['include/absl'],
+}
+
+moduleclass = 'lib'

From 8050e2bdaacd19ae00b5f1ad6cc529ecda39bd49 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 5 May 2023 00:48:43 +0200
Subject: [PATCH 480/601] Update
 easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb

---
 .../easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb
index adb4b6dc91d..a94e4236997 100644
--- a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb
@@ -23,7 +23,7 @@ builddependencies = [
 
 sanity_check_paths = {
     'files': ['bin/rocm-smi'],
-    'dirs': [''],
+    'dirs': [],
 }
 
 sanity_check_commands = ['rocm-smi --help']

From 558a424a3f3ee742693ce587573a308faac448ca Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 5 May 2023 09:14:03 +0200
Subject: [PATCH 481/601] remove versionsuffix

---
 .../c/CellChat/CellChat-1.5.0-foss-2022a.eb   | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb
new file mode 100644
index 00000000000..8b0c66ef249
--- /dev/null
+++ b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb
@@ -0,0 +1,56 @@
+easyblock = 'Bundle'
+
+name = 'CellChat'
+version = '1.5.0'
+
+homepage = 'https://github.com/sqjin/CellChat'
+description = """"
+R toolkit for inference, visualization and analysis of cell-cell communication
+from single-cell data"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('umap-learn', '0.5.3'),
+]
+
+exts_defaultclass = 'RPackage'
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+}
+
+exts_list = [
+    ('ggalluvial', '0.12.5', {
+        'checksums': ['90044c880e70096137a733d601b11e558fe55e4e7d3aaacac6f08d7847415d71'],
+    }),
+    ('systemfonts', '1.0.4', {
+        'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'],
+    }),
+    ('svglite', '2.1.1', {
+        'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'],
+    }),
+    (name, version, {
+        'preinstallopts': "rm src/*.o src/*.so && ",
+        'source_urls': ['https://github.com/sqjin/CellChat/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['c9e31327cbbcf1fec5e6d8a0dfe011ded8e543557107e93dd4a417c4c137d1c6'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'bio'

From ca79d6add74b5338e0e5ee2d885d3c4a9c190485 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 5 May 2023 09:15:22 +0200
Subject: [PATCH 482/601] remove versionsuffix

---
 .../CellChat-1.5.0-foss-2022a-R-4.2.1.eb      | 57 -------------------
 1 file changed, 57 deletions(-)
 delete mode 100644 easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb
deleted file mode 100644
index 97b28ca1651..00000000000
--- a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb
+++ /dev/null
@@ -1,57 +0,0 @@
-easyblock = 'Bundle'
-
-name = 'CellChat'
-version = '1.5.0'
-versionsuffix = '-R-%(rver)s'
-
-homepage = 'https://github.com/sqjin/CellChat'
-description = """"
-R toolkit for inference, visualization and analysis of cell-cell communication
-from single-cell data"""
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-dependencies = [
-    ('R', '4.2.1'),
-    ('R-bundle-Bioconductor', '3.15', versionsuffix),
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('umap-learn', '0.5.3'),
-]
-
-exts_defaultclass = 'RPackage'
-exts_default_options = {
-    'sources': ['%(name)s_%(version)s.tar.gz'],
-    'source_urls': [
-        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
-        'https://cran.r-project.org/src/contrib/',  # current version of packages
-        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
-    ],
-}
-
-exts_list = [
-    ('ggalluvial', '0.12.5', {
-        'checksums': ['90044c880e70096137a733d601b11e558fe55e4e7d3aaacac6f08d7847415d71'],
-    }),
-    ('systemfonts', '1.0.4', {
-        'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'],
-    }),
-    ('svglite', '2.1.1', {
-        'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'],
-    }),
-    (name, version, {
-        'preinstallopts': "rm src/*.o src/*.so && ",
-        'source_urls': ['https://github.com/sqjin/CellChat/archive/'],
-        'sources': ['v%(version)s.tar.gz'],
-        'checksums': ['c9e31327cbbcf1fec5e6d8a0dfe011ded8e543557107e93dd4a417c4c137d1c6'],
-    }),
-]
-
-sanity_check_paths = {
-    'files': [],
-    'dirs': [name],
-}
-
-modextrapaths = {'R_LIBS_SITE': ''}
-
-moduleclass = 'bio'

From 5c4debc9532d6f1f1ffc3fa4133f932b235683cb Mon Sep 17 00:00:00 2001
From: Vital-IT <vitsoft@sib.swiss>
Date: Fri, 5 May 2023 10:06:17 +0200
Subject: [PATCH 483/601] adding easyconfigs: AGeNT-3.0.6.eb

---
 easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb | 69 ++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb

diff --git a/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb
new file mode 100644
index 00000000000..545544653f1
--- /dev/null
+++ b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb
@@ -0,0 +1,69 @@
+##
+# This is a contribution from SIB Swiss Institute of Bioinformatics
+# Homepage:     https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
+#
+# Authors::     Sebastien Moretti <sebastien.moretti@sib.swiss>
+#
+##
+
+# JAR files are in a subdirectory with other stuff, so use Binary
+easyblock = 'Binary'
+
+name = 'AGeNT'
+version = '3.0.6'
+
+homepage = 'https://www.agilent.com/en/product/next-generation-sequencing/'
+homepage += 'hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879'
+description = """The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software
+module that processes the read sequences from targeted high-throughput sequencing data
+generated by sequencing Agilent SureSelect and HaloPlex libraries.
+
+The Trimmer utility of the AGeNT module processes the read sequences to identify and
+remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2).
+
+The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information
+from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with
+options to either mark or merge duplicate reads and output in BAM file format. The Illumina
+InterOp libraries are a set of common routines used for reading InterOp metric files
+produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards
+compatible and capable of supporting prior releases of the software, with one exception:
+GA systems have been excluded."""
+
+software_license = 'LicenseVeryRestrictive'
+# For Research Use Only. Not for use in diagnostic procedures.
+
+toolchain = SYSTEM
+
+builddependencies = [
+    ('UnZip', '6.0', '', ('GCCcore', '10.3.0')),
+]
+dependencies = [
+    ('Java', '11'),
+]
+
+# Fill the form at https://explore.agilent.com/AGeNT-Software-Download-Form
+# to get the zip file.
+sources = ['AGeNT_%(version)s.zip']
+checksums = ['746e4445567ee41b7ced5cab3cd252d27d8f6f9eab56766e5d7ca74894e3db73']
+
+extract_sources = False
+
+install_cmd = 'unzip ' + sources[0] + ' && '
+install_cmd += 'cp -ar *.html *.md agent/* %(installdir)s/ && '
+install_cmd += 'find %(installdir)s/ -type f -name \*.txt  -exec chmod -x {} \; && '
+install_cmd += 'find %(installdir)s/ -type f -name \*.md   -exec chmod -x {} \; && '
+install_cmd += 'find %(installdir)s/ -type f -name \*.cmd  -exec rm    -f {} \; && '
+install_cmd += 'find %(installdir)s/ -type f -name \*.html -exec rm    -f {} \; && '
+install_cmd += 'mkdir %(installdir)s/bin && '
+install_cmd += 'mv %(installdir)s/*.sh %(installdir)s/bin/ && '
+install_cmd += 'ln -s ../lib %(installdir)s/bin/lib && '
+install_cmd += 'sed -i "s@ lib/@ ../lib/@" %(installdir)s/bin/*.sh'
+
+sanity_check_paths = {
+    'files': ['bin/agent.sh'],
+    'dirs': ['bin', 'lib']
+}
+
+sanity_check_commands = ["agent.sh"]
+
+moduleclass = 'bio'

From cefd6e365f5e22518dd84822841abf907a44a73b Mon Sep 17 00:00:00 2001
From: Vital-IT <vitsoft@sib.swiss>
Date: Fri, 5 May 2023 10:36:53 +0200
Subject: [PATCH 484/601] Fix Static Analysis issues

---
 easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb
index 545544653f1..c176dbde77c 100644
--- a/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb
+++ b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb
@@ -50,10 +50,10 @@ extract_sources = False
 
 install_cmd = 'unzip ' + sources[0] + ' && '
 install_cmd += 'cp -ar *.html *.md agent/* %(installdir)s/ && '
-install_cmd += 'find %(installdir)s/ -type f -name \*.txt  -exec chmod -x {} \; && '
-install_cmd += 'find %(installdir)s/ -type f -name \*.md   -exec chmod -x {} \; && '
-install_cmd += 'find %(installdir)s/ -type f -name \*.cmd  -exec rm    -f {} \; && '
-install_cmd += 'find %(installdir)s/ -type f -name \*.html -exec rm    -f {} \; && '
+install_cmd += 'chmod -x %(installdir)s/*.txt && '
+install_cmd += 'chmod -x %(installdir)s/*.md && '
+install_cmd += 'rm -f %(installdir)s/*.cmd && '
+install_cmd += 'rm -f %(installdir)s/*.html && '
 install_cmd += 'mkdir %(installdir)s/bin && '
 install_cmd += 'mv %(installdir)s/*.sh %(installdir)s/bin/ && '
 install_cmd += 'ln -s ../lib %(installdir)s/bin/lib && '

From bc8a6f0eff3a9328b1c80f629f8c6741d22d791e Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Fri, 5 May 2023 10:41:01 +0100
Subject: [PATCH 485/601] adding easyconfigs: Triplexator-1.3.3-GCC-11.2.0.eb
 and patches: Triplexator-1.3.3_support-modern-compilers.patch

---
 .../Triplexator-1.3.3-GCC-11.2.0.eb           |  43 +++++++
 ...xator-1.3.3_support-modern-compilers.patch | 113 ++++++++++++++++++
 2 files changed, 156 insertions(+)
 create mode 100755 easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb
 create mode 100755 easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch

diff --git a/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb
new file mode 100755
index 00000000000..4a007546c50
--- /dev/null
+++ b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb
@@ -0,0 +1,43 @@
+# This easyconfig was created by the BEAR Software team at the University of Birmingham.
+easyblock = 'CMakeMake'
+
+name = 'Triplexator'
+version = '1.3.3'
+
+homepage = "https://github.com/Gurado/triplexator"
+description = """Triplexator is a tool for detecting nucleic acid triple helices and triplex features in nucleotide
+ sequences using the canonical triplex-formation rules."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+github_account = 'Gurado'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['Triplexator-1.3.3_support-modern-compilers.patch']
+checksums = [
+    {'v1.3.3.tar.gz': '24b862062ea36bef67beaa9fcade7860450f98c14dcfa499fca666e2b8c570b2'},
+    {'Triplexator-1.3.3_support-modern-compilers.patch':
+     '1c2bee4aab6693c1f5836eb1688a4345b1ff5fa22333bf3252eb749f15995e64'},
+]
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+]
+
+dependencies = [
+    ('Boost', '1.79.0'),
+]
+
+# The above patch makes the code buildable with CMAKE_CXX_STANDARD 11, so set that here
+configopts = '-DCMAKE_CXX_STANDARD=11'
+
+sanity_check_commands = [
+    "cd %(builddir)s/%(namelower)s-%(version)s && ./demos/smoketest_triplexator.sh %(installdir)s/bin/%(namelower)s"
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch
new file mode 100755
index 00000000000..3a10a3a2639
--- /dev/null
+++ b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch
@@ -0,0 +1,113 @@
+From e1f86e7df06dd53f0af242858db3909eaa35dac6 Mon Sep 17 00:00:00 2001
+From: amatria <i.amatria@udc.es>
+Date: Thu, 8 Sep 2022 12:41:02 +0200
+Subject: [PATCH] compile with a modern c++ compiler
+
+---
+ src/seqan/file/file_format.h                  | 32 +++++++++----------
+ .../parallel/parallel_generated_forwards.h    |  2 +-
+ src/seqan/parallel/parallel_splitting.h       |  6 ++--
+ src/triplexator.cpp                           |  4 +--
+ 4 files changed, 23 insertions(+), 21 deletions(-)
+
+diff --git a/src/seqan/file/file_format.h b/src/seqan/file/file_format.h
+index da64632..d6df116 100644
+--- a/src/seqan/file/file_format.h
++++ b/src/seqan/file/file_format.h
+@@ -205,27 +205,27 @@ struct FileFormat<TFile, TData, TMeta, void>
+ 	~FileFormat() {}
+ 	FileFormat const & operator =(FileFormat const &) { return *this; }
+ 
+-	virtual void *
+-	formatID_() const = 0;
++	void *
++	formatID_();
+ 
+-	virtual void
+-	read_(TFile & file, TData & data) const = 0;
+-	virtual void
+-	read_(TFile & file, TData & data, TSize limit) const = 0;
++	void
++	read_(TFile & file, TData & data);
++	void
++	read_(TFile & file, TData & data, TSize limit);
+ 
+-	virtual void
+-	readMeta_(TFile & file, TMeta & meta) const = 0;
++	void
++	readMeta_(TFile & file, TMeta & meta);
+ 
+-	virtual void
+-	goNext_(TFile & file) const = 0;
++	void
++	goNext_(TFile & file);
+ 
+-	virtual TSize
+-	length_(TFile & file) const = 0;
++	TSize
++	length_(TFile & file);
+ 
+-	virtual void
+-	write_(TFile & file, TData & data) const = 0;
+-	virtual void
+-	write_(TFile & file, TData & data, TMeta & meta) const = 0;
++	void
++	write_(TFile & file, TData & data);
++	void
++	write_(TFile & file, TData & data, TMeta & meta);
+ 
+ };
+ 
+diff --git a/src/seqan/parallel/parallel_generated_forwards.h b/src/seqan/parallel/parallel_generated_forwards.h
+index 78e9e3e..682bd45 100644
+--- a/src/seqan/parallel/parallel_generated_forwards.h
++++ b/src/seqan/parallel/parallel_generated_forwards.h
+@@ -57,7 +57,7 @@ namespace seqan {
+ //____________________________________________________________________________
+ // computeSplitters
+ 
+-template <typename TPos, typename TSize, typename TCount> void computeSplitters(String<TPos> & splitters, TSize size, TCount count);       	// "/Users/fabianbuske/Documents/research/triplex/seqan/core/include/seqan/parallel/parallel_splitting.h"(64)
++template <typename TPosString, typename TSize, typename TCount> void computeSplitters(TPosString & splitters, TSize size, TCount count);       	// "/Users/fabianbuske/Documents/research/triplex/seqan/core/include/seqan/parallel/parallel_splitting.h"(64)
+ 
+ } //namespace seqan
+ 
+diff --git a/src/seqan/parallel/parallel_splitting.h b/src/seqan/parallel/parallel_splitting.h
+index f8d862f..1ed786d 100755
+--- a/src/seqan/parallel/parallel_splitting.h
++++ b/src/seqan/parallel/parallel_splitting.h
+@@ -59,9 +59,11 @@ computeSplitters(splitters, 10, 5);
+ ..include:seqan/parallel.h
+  */
+ 
+-template <typename TPos, typename TSize, typename TCount>
+-void computeSplitters(String<TPos> & splitters, TSize size, TCount count)
++template <typename TPosString, typename TSize, typename TCount>
++void computeSplitters(TPosString & splitters, TSize size, TCount count)
+ {
++    typedef typename Value<TPosString>::Type TPos;
++
+     resize(splitters, count + 1);
+     splitters[0] = 0;
+     TSize blockLength = size / count;
+diff --git a/src/triplexator.cpp b/src/triplexator.cpp
+index a3738cb..d6d8e7f 100644
+--- a/src/triplexator.cpp
++++ b/src/triplexator.cpp
+@@ -917,7 +917,7 @@ namespace SEQAN_NAMESPACE_MAIN
+ 			appendValue(duplexNames, id, Generous());
+ 			
+ 			read(file, duplexString, Fasta());			// read Fasta sequence
+-			ttsnoToFileMap.insert(::std::make_pair<unsigned,::std::pair< ::std::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
++			ttsnoToFileMap.insert(::std::make_pair<unsigned,::std::pair< ::std::string,unsigned> >(::std::move(seqNo),::std::make_pair< ::std::string,unsigned>(::std::move(filename),::std::move(seqNoWithinFile))));
+ 			
+ 			if (options._debugLevel > 1 )
+ 				options.logFileHandle << _getTimeStamp() << "   ... Finished reading next duplex sequence" << ::std::endl;
+@@ -1040,7 +1040,7 @@ namespace SEQAN_NAMESPACE_MAIN
+ 			readShortID(file, id, Fasta());			// read Fasta id up to first whitespace
+ 			appendValue(duplexNames, id, Generous());
+ 			read(file, duplexString, Fasta());		// read Fasta sequence
+-			ttsnoToFileMap.insert(::std::make_pair<unsigned,::std::pair< ::std::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
++			ttsnoToFileMap.insert(::std::make_pair<unsigned,::std::pair< ::std::string,unsigned> >(::std::move(seqNo),::std::make_pair< ::std::string,unsigned>(::std::move(filename),::std::move(seqNoWithinFile))));
+ 			appendValue(duplexSet, duplexString);	
+ 			
+ 			if (options._debugLevel > 1 )

From 91e9b05b34f79dd8989a446205ea4086b1fab32e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 5 May 2023 14:45:28 +0200
Subject: [PATCH 486/601] remove unnecessary deps

---
 .../easyconfigs/b/build/build-0.10.0-foss-2022a.eb   |  9 ---------
 .../pod5-file-format-0.1.8-foss-2022a.eb             | 12 ++++++------
 .../pod5-file-format-0.1.8_dep_fix.patch             |  3 +++
 3 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb
index ce8f9a50a22..4c80ab3d18f 100644
--- a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb
@@ -16,15 +16,6 @@ use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    ('pyparsing', '3.0.9', {
-        'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'],
-    }),
-    ('packaging', '20.4', {
-        'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'],
-    }),
-    ('tomli', '2.0.1', {
-        'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'],
-    }),
     ('pyproject_hooks', '1.0.0', {
         'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'],
     }),
diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
index 5804c85e8ec..e1c12919d47 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb
@@ -15,12 +15,13 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ
 patches = ['pod5-file-format-0.1.8_dep_fix.patch']
 checksums = [
     {'pod5-file-format-0.1.8.tar.gz': '262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'},
-    {'pod5-file-format-0.1.8_dep_fix.patch': 'd24fab7477d735ba7bb4a286c7a64d6138bf6a82a5a021b257eeeb5dfa06d82e'},
+    {'pod5-file-format-0.1.8_dep_fix.patch': '9c7fe8e8aa79c8fff9e43ea3ae1754c5ef0d3023c47f7e4a157d12b34be378a4'},
 ]
 
 builddependencies = [
     ('binutils', '2.38'),
     ('CMake', '3.23.1'),
+    ('pkgconfig', '1.5.5', '-python'),
 ]
 
 dependencies = [
@@ -32,7 +33,6 @@ dependencies = [
     ('pybind11', '2.9.2'),
     ('Boost', '1.79.0'),
     ('build', '0.10.0'),
-    ('pkg-config', '0.29.2'),
     ('HDF5', '1.12.2'),
     ('h5py', '3.7.0'),
 ]
@@ -47,9 +47,6 @@ exts_default_options = {
 }
 
 exts_list = [
-    ('pkgconfig', '1.5.5', {
-        'checksums': ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'],
-    }),
     ('attrs', '22.2.0', {
         'checksums': ['c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99'],
     }),
@@ -79,7 +76,10 @@ sanity_check_paths = {
     'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'],
 }
 
-sanity_check_commands = ['pod5 subset --help']
+sanity_check_commands = [
+    "pod5 subset --help",
+    "python -c 'import lib_pod5'",
+]
 
 modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
 
diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
index f9430ef0310..3015c600bb5 100644
--- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
+++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch
@@ -1,3 +1,6 @@
+Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake'
+We want to use our pybind11 instead of the one in git submodules
+Author: Petr Král (INUITS)
 diff -u pod5-file-format-0.1.8/c++/CMakeLists.txt.orig pod5-file-format-0.1.8/c++/CMakeLists.txt
 --- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig      2023-02-23 19:17:13.000000000 +0100
 +++ pod5-file-format-0.1.8/c++/CMakeLists.txt   2023-04-25 14:07:28.174884834 +0200

From 84fc5207c2af70c20ea2f8fe931ba04d28473b0b Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 5 May 2023 15:37:17 +0200
Subject: [PATCH 487/601] Move FLINT to gfbf/foss level.

---
 .../f/FLINT/FLINT-2.8.4-foss-2021b.eb         | 46 +++++++++++++++++++
 .../f/FLINT/FLINT-2.8.4_find_flexiblas.patch  | 23 ++++++++++
 .../f/FLINT/FLINT-2.9.0-gfbf-2022a.eb         | 42 +++++++++++++++++
 .../n/NTL/NTL-11.5.1-GCC-11.2.0.eb            | 44 ++++++++++++++++++
 .../n/NTL/NTL-11.5.1-GCC-11.3.0.eb            | 44 ++++++++++++++++++
 5 files changed, 199 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb
 create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch
 create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb
 create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb
 create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb
new file mode 100644
index 00000000000..493b0f97e4f
--- /dev/null
+++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb
@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'FLINT'
+version = '2.8.4'
+
+homepage = 'https://www.flintlib.org/'
+
+description = """FLINT (Fast Library for Number Theory) is a C library in support of computations
+ in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs,
+ factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides
+ various low-level routines for fast arithmetic. FLINT is extensively documented and tested."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.flintlib.org']
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    '%(name)s-%(version)s_find_flexiblas.patch',
+]
+checksums = [
+    {'flint-2.8.4.tar.gz': '61df92ea8c8e9dc692d46c71d7f50aaa09a33d4ba08d02a1784730a445e5e4be'},
+    {'FLINT-2.8.4_find_flexiblas.patch': '35a3db14646daf584449f2b9c6880b66e7b082a665eba56234230610bab77c6e'},
+]
+
+builddependencies = [
+    ('CMake', '3.22.1'),
+    ('Python', '3.9.6'),
+]
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.1.0'),
+    ('NTL', '11.5.1'),
+]
+
+configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes'
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch
new file mode 100644
index 00000000000..54412d05b23
--- /dev/null
+++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch
@@ -0,0 +1,23 @@
+Use FlexiBLAS when available
+
+Åke Sandgren, 2023-05-03
+diff -ru flint-2.8.4.orig/CMake/FindCBLAS.cmake flint-2.8.4/CMake/FindCBLAS.cmake
+--- flint-2.8.4.orig/CMake/FindCBLAS.cmake	2021-11-17 18:43:50.000000000 +0100
++++ flint-2.8.4/CMake/FindCBLAS.cmake	2023-05-03 09:29:36.599062848 +0200
+@@ -11,13 +11,13 @@
+ find_path(CBLAS_INCLUDE_DIRS NAMES cblas.h
+   HINTS CBLAS_ROOT ENV CBLAS_ROOT
+   PATHS ${INCLUDE_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/include
+-  PATH_SUFFIXES openblas cblas blis
++  PATH_SUFFIXES flexiblas openblas cblas blis
+   )
+ 
+-find_library(CBLAS_LIBRARIES NAMES accelerate openblas cblas blas blis
++find_library(CBLAS_LIBRARIES NAMES accelerate flexiblas openblas cblas blas blis
+   HINTS CBLAS_ROOT ENV CBLAS_ROOT
+   PATHS ${LIB_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/lib
+-  PATH_SUFFIXES openblas cblas blis
++  PATH_SUFFIXES flexiblas openblas cblas blis
+   )
+ 
+ include(FindPackageHandleStandardArgs)
diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb
new file mode 100644
index 00000000000..8d6bb6cc6fb
--- /dev/null
+++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb
@@ -0,0 +1,42 @@
+easyblock = 'CMakeMake'
+
+name = 'FLINT'
+version = '2.9.0'
+
+homepage = 'https://www.flintlib.org/'
+
+description = """FLINT (Fast Library for Number Theory) is a C library in support of computations
+ in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs,
+ factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides
+ various low-level routines for fast arithmetic. FLINT is extensively documented and tested."""
+
+toolchain = {'name': 'gfbf', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.flintlib.org']
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    '%(name)s-2.8.4_find_flexiblas.patch',
+]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('Python', '3.10.4'),
+]
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.1.0'),
+    ('NTL', '11.5.1'),
+]
+
+configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes'
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb
new file mode 100644
index 00000000000..cbeb836cd91
--- /dev/null
+++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb
@@ -0,0 +1,44 @@
+# contributed by Guilherme Peretti-Pezzi (CSCS)
+# updated by Alex Domingo (Vrije Universiteit Brussel)
+# updated by Åke Sandgren(Umeå University)
+
+easyblock = 'ConfigureMake'
+
+name = 'NTL'
+version = '11.5.1'
+
+homepage = 'https://shoup.net/ntl/'
+
+description = """NTL is a high-performance, portable C++ library providing data structures and
+algorithms for manipulating signed, arbitrary length integers, and for vectors,
+matrices, and polynomials over the integers and over finite fields."""
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'libntl'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5']
+
+builddependencies = [
+    ('Perl', '5.34.0'),
+]
+
+dependencies = [
+    ('GMP', '6.2.1'),
+]
+
+start_dir = 'src'
+
+prefix_opt = 'PREFIX='
+configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]],
+    'dirs': ['include/NTL', 'share/doc'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb
new file mode 100644
index 00000000000..89c7288994f
--- /dev/null
+++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb
@@ -0,0 +1,44 @@
+# contributed by Guilherme Peretti-Pezzi (CSCS)
+# updated by Alex Domingo (Vrije Universiteit Brussel)
+# updated by Åke Sandgren(Umeå University)
+
+easyblock = 'ConfigureMake'
+
+name = 'NTL'
+version = '11.5.1'
+
+homepage = 'https://shoup.net/ntl/'
+
+description = """NTL is a high-performance, portable C++ library providing data structures and
+algorithms for manipulating signed, arbitrary length integers, and for vectors,
+matrices, and polynomials over the integers and over finite fields."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'libntl'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5']
+
+builddependencies = [
+    ('Perl', '5.34.1'),
+]
+
+dependencies = [
+    ('GMP', '6.2.1'),
+]
+
+start_dir = 'src'
+
+prefix_opt = 'PREFIX='
+configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]],
+    'dirs': ['include/NTL', 'share/doc'],
+}
+
+moduleclass = 'math'

From 4304c1a1e067884325dcb5aba7e0347f19852687 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 5 May 2023 15:42:06 +0200
Subject: [PATCH 488/601] FLINT: Drop GCC level easyconfigs for GCC
 11.2.0/11.3.0 They should be at gfbf/foss level depending on toolchain
 version due to BLAS being a depedency.

---
 .../f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb         | 34 -------------------
 .../f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb         | 34 -------------------
 2 files changed, 68 deletions(-)
 delete mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb
 delete mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb
deleted file mode 100644
index 8b3d55e165d..00000000000
--- a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb
+++ /dev/null
@@ -1,34 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'FLINT'
-version = '2.8.4'
-
-homepage = 'https://www.flintlib.org/'
-
-description = """FLINT (Fast Library for Number Theory) is a C library in support of computations
- in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs,
- factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides
- various low-level routines for fast arithmetic. FLINT is extensively documented and tested."""
-
-toolchain = {'name': 'GCC', 'version': '11.2.0'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://www.flintlib.org']
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['61df92ea8c8e9dc692d46c71d7f50aaa09a33d4ba08d02a1784730a445e5e4be']
-
-builddependencies = [
-    ('CMake', '3.22.1'),
-]
-
-dependencies = [
-    ('GMP', '6.2.1'),
-    ('MPFR', '4.1.0'),
-]
-
-sanity_check_paths = {
-    'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT],
-    'dirs': ['include'],
-}
-
-moduleclass = 'math'
diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb
deleted file mode 100644
index 90131d5e4c4..00000000000
--- a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb
+++ /dev/null
@@ -1,34 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'FLINT'
-version = '2.9.0'
-
-homepage = 'https://www.flintlib.org/'
-
-description = """FLINT (Fast Library for Number Theory) is a C library in support of computations
- in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs,
- factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides
- various low-level routines for fast arithmetic. FLINT is extensively documented and tested."""
-
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
-toolchainopts = {'pic': True}
-
-source_urls = ['https://www.flintlib.org']
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['2fc090d51033c93208e6c10d406397a53c983ae5343b958eb25f72a57a4ce76a']
-
-builddependencies = [
-    ('CMake', '3.23.1'),
-]
-
-dependencies = [
-    ('GMP', '6.2.1'),
-    ('MPFR', '4.1.0'),
-]
-
-sanity_check_paths = {
-    'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT],
-    'dirs': ['include'],
-}
-
-moduleclass = 'math'

From c3d1da0b78ef4590d3151335d02200d802242c50 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 5 May 2023 16:16:50 +0200
Subject: [PATCH 489/601] Move Arb and polymake to gfbf/foss level.

---
 .../a/Arb/Arb-2.22.1-foss-2021b.eb            | 35 ++++++++++++++++++
 .../a/Arb/Arb-2.23.0-gfbf-2022a.eb            | 35 ++++++++++++++++++
 .../p/polymake/polymake-4.8-foss-2021b.eb     | 37 +++++++++++++++++++
 .../p/polymake/polymake-4.8-gfbf-2022a.eb     | 37 +++++++++++++++++++
 .../easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb  | 26 +++++++++++++
 5 files changed, 170 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb
 create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb
 create mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb
 create mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb
 create mode 100644 easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb

diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb
new file mode 100644
index 00000000000..6aede555b93
--- /dev/null
+++ b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'Arb'
+version = '2.22.1'
+
+homepage = 'https://arblib.org/'
+
+description = """Arb is a C library for arbitrary-precision interval arithmetic.
+ It has full support for both real and complex numbers. The library is thread-safe,
+ portable, and extensively tested."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+toolchainopts = {'pic': True}
+
+github_account = 'fredrik-johansson'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['1ef85518eee04885e8a90196498bc75e4e2410621d4184f2bc01d46b7080a243']
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.1.0'),
+    ('FLINT', '2.8.4'),
+]
+
+configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb b/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb
new file mode 100644
index 00000000000..06c0fa3ab76
--- /dev/null
+++ b/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'Arb'
+version = '2.23.0'
+
+homepage = 'https://arblib.org/'
+
+description = """Arb is a C library for arbitrary-precision interval arithmetic.
+ It has full support for both real and complex numbers. The library is thread-safe,
+ portable, and extensively tested."""
+
+toolchain = {'name': 'gfbf', 'version': '2022a'}
+toolchainopts = {'pic': True}
+
+github_account = 'fredrik-johansson'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['977d41bde46f5442511d5165c705cec32c03e852c84d7d1836135d412ce702bb']
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.1.0'),
+    ('FLINT', '2.9.0'),
+]
+
+configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR'
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb
new file mode 100644
index 00000000000..a15d42eeece
--- /dev/null
+++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'polymake'
+version = '4.8'
+
+homepage = 'https://polymake.org'
+description = """polymake is open source software for research in polyhedral geometry.
+It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids,
+graphs, tropical hypersurfaces, and other objects."""
+
+toolchain = {'name': 'foss', 'version': '2021b'}
+
+source_urls = ['https://polymake.org/lib/exe/fetch.php/download/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11']
+
+dependencies = [
+    ('Ninja', '1.10.2'),
+    ('libxml2', '2.9.10'),
+    ('libxslt', '1.1.34'),
+    ('libreadline', '8.1'),
+    ('Perl', '5.34.0'),
+    ('SVG', '2.87'),
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.1.0'),
+    ('Boost', '1.77.0'),
+    ('FLINT', '2.8.4'),
+    ('Java', '11', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT,
+              'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT],
+    'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb
new file mode 100644
index 00000000000..5eff12ad133
--- /dev/null
+++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'polymake'
+version = '4.8'
+
+homepage = 'https://polymake.org'
+description = """polymake is open source software for research in polyhedral geometry.
+It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids,
+graphs, tropical hypersurfaces, and other objects."""
+
+toolchain = {'name': 'gfbf', 'version': '2022a'}
+
+source_urls = ['https://polymake.org/lib/exe/fetch.php/download/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11']
+
+dependencies = [
+    ('Ninja', '1.10.2'),
+    ('libxml2', '2.9.13'),
+    ('libxslt', '1.1.34'),
+    ('libreadline', '8.1.2'),
+    ('Perl', '5.34.1'),
+    ('SVG', '2.87'),
+    ('GMP', '6.2.1'),
+    ('MPFR', '4.1.0'),
+    ('Boost', '1.79.0'),
+    ('FLINT', '2.9.0'),
+    ('Java', '11', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT,
+              'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT],
+    'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb
new file mode 100644
index 00000000000..1eaefad2e9d
--- /dev/null
+++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'PerlModule'
+
+name = 'SVG'
+version = '2.87'
+
+homepage = 'https://metacpan.org/pod/SVG'
+description = "Perl binding for SVG"
+
+toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c']
+
+dependencies = [
+    ('Perl', '5.34.0'),
+]
+
+options = {'modulename': 'SVG'}
+
+sanity_check_paths = {
+    'files': ['lib/perl5/site_perl/%(perlver)s/SVG.pm'],
+    'dirs': ['lib/perl5/site_perl/%(perlver)s/SVG'],
+}
+
+moduleclass = 'data'

From 580a723e3e361f3a5988dfc34da0be2488d35adc Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Fri, 5 May 2023 16:21:29 +0200
Subject: [PATCH 490/601] Drop Arb and polymake at GCC level since FLINT is now
 at gfbf/foss New Arb and polymake versions in PR #17869

---
 .../a/Arb/Arb-2.22.1-GCC-11.2.0.eb            | 35 ------------------
 .../p/polymake/polymake-4.8-GCC-11.3.0.eb     | 37 -------------------
 2 files changed, 72 deletions(-)
 delete mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb
 delete mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb
deleted file mode 100644
index f729c96081d..00000000000
--- a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb
+++ /dev/null
@@ -1,35 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'Arb'
-version = '2.22.1'
-
-homepage = 'https://arblib.org/'
-
-description = """Arb is a C library for arbitrary-precision interval arithmetic.
- It has full support for both real and complex numbers. The library is thread-safe,
- portable, and extensively tested."""
-
-toolchain = {'name': 'GCC', 'version': '11.2.0'}
-toolchainopts = {'pic': True}
-
-github_account = 'fredrik-johansson'
-source_urls = [GITHUB_LOWER_SOURCE]
-sources = ['%(version)s.tar.gz']
-checksums = ['1ef85518eee04885e8a90196498bc75e4e2410621d4184f2bc01d46b7080a243']
-
-dependencies = [
-    ('FLINT', '2.8.4'),
-    ('GMP', '6.2.1'),
-    ('MPFR', '4.1.0'),
-]
-
-configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR'
-
-runtest = 'check'
-
-sanity_check_paths = {
-    'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'],
-    'dirs': ['include'],
-}
-
-moduleclass = 'math'
diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb
deleted file mode 100644
index bb766d01955..00000000000
--- a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb
+++ /dev/null
@@ -1,37 +0,0 @@
-easyblock = 'ConfigureMake'
-
-name = 'polymake'
-version = '4.8'
-
-homepage = 'https://polymake.org'
-description = """polymake is open source software for research in polyhedral geometry.
-It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids,
-graphs, tropical hypersurfaces, and other objects."""
-
-toolchain = {'name': 'GCC', 'version': '11.3.0'}
-
-source_urls = ['https://polymake.org/lib/exe/fetch.php/download/']
-sources = [SOURCE_TAR_BZ2]
-checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11']
-
-dependencies = [
-    ('Ninja', '1.10.2'),
-    ('libxml2', '2.9.13'),
-    ('libxslt', '1.1.34'),
-    ('libreadline', '8.1.2'),
-    ('Perl', '5.34.1'),
-    ('SVG', '2.87'),
-    ('GMP', '6.2.1'),
-    ('MPFR', '4.1.0'),
-    ('Boost', '1.79.0'),
-    ('FLINT', '2.9.0'),
-    ('Java', '11', '', SYSTEM),
-]
-
-sanity_check_paths = {
-    'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT,
-              'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT],
-    'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'],
-}
-
-moduleclass = 'math'

From 7eebeef97c90c71ac8c75cf5ca71a47f97978a1a Mon Sep 17 00:00:00 2001
From: Ben Langenberg <ben.langenberg@ufz.de>
Date: Fri, 5 May 2023 17:28:41 +0200
Subject: [PATCH 491/601] adding easyconfigs: HDF5-1.10.6-iompi-2020a.eb

---
 .../h/HDF5/HDF5-1.10.6-iompi-2020a.eb         | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb

diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb
new file mode 100644
index 00000000000..6c000f1179e
--- /dev/null
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb
@@ -0,0 +1,22 @@
+name = 'HDF5'
+version = '1.10.6'
+
+homepage = 'https://portal.hdfgroup.org/display/support'
+description = """HDF5 is a data model, library, and file format for storing and managing data.
+ It supports an unlimited variety of datatypes, and is designed for flexible
+ and efficient I/O and for high volume and complex data."""
+
+toolchain = {'name': 'iompi', 'version': '2020a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa']
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Szip', '2.1.1'),
+]
+
+moduleclass = 'data'
+

From cbb0bcd11f34117536dd4d5c8552c84571670e1d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 5 May 2023 18:26:01 +0200
Subject: [PATCH 492/601] Update
 easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb

---
 easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb
index 6c000f1179e..ddde88aa068 100644
--- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb
@@ -19,4 +19,3 @@ dependencies = [
 ]
 
 moduleclass = 'data'
-

From 69e3e594c1f82e93e1c5ec803c67ad8905ce1795 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Sat, 6 May 2023 14:29:41 +0200
Subject: [PATCH 493/601] Update
 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

thanks, didnt notice

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
index 9bcd7cf4116..e2ffcd2d854 100644
--- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
@@ -7,7 +7,7 @@ name = 'CPC2'
 version = '0.1'
 local_commit = '813487e'
 
-homepage = 'http://cpc2.cbi.pku.edu.cn'
+homepage = 'http://cpc2.gao-lab.org/'
 description = """ a fast and accurate coding potential calculator based on sequence intrinsic features  """
 
 toolchain = {'name': 'foss', 'version': '2022a'}

From 9f1c0513aebfc0458cd2863d34c820580d1e4123 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Sat, 6 May 2023 21:23:16 +0200
Subject: [PATCH 494/601] adding easyconfigs: gpustat-1.1-GCCcore-11.3.0.eb

---
 .../g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb   | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..a581373ba1e
--- /dev/null
+++ b/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'PythonBundle'
+
+name = 'gpustat'
+version = '1.1'
+
+homepage = 'https://github.com/wookayin/gpustat'
+description = "A simple command-line utility for querying and monitoring GPU status"
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+# This software works directly against the nvidia drivers and doesn't require CUDA.
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('blessed', '1.20.0', {
+        'checksums': ['2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680'],
+    }),
+    ('nvidia-ml-py', '11.525.112', {
+        'modulename': 'pynvml',
+        'checksums': ['c64e473953b65ec0ccc76cf3601c3130a0ac8060bbcaea912cc00fa8e4c9868d'],
+    }),
+    (name, version, {
+        'checksums': ['c8fc105404aac11884f70ed2fa06cfd210d3cd389ccae4a9bc38579c72460cee'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gpustat'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["gpustat --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 2f66aedb8f2f1628790bdf0c36b67865c5bbcd31 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 8 May 2023 08:23:38 +0200
Subject: [PATCH 495/601] adding easyconfigs: ReFrame-4.2.0.eb

---
 .../easyconfigs/r/ReFrame/ReFrame-4.2.0.eb    | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb

diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb
new file mode 100644
index 00000000000..dc290fcc04d
--- /dev/null
+++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb
@@ -0,0 +1,63 @@
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+easyblock = 'PythonBundle'
+
+name = 'ReFrame'
+version = '4.2.0'
+
+homepage = 'https://github.com/reframe-hpc/reframe'
+description = '''ReFrame is a framework for writing regression tests for HPC systems.'''
+
+toolchain = SYSTEM
+
+allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+req_py_majver = 3
+req_py_minver = 6
+
+use_pip = True
+
+exts_list = [
+    ('pip', '21.3.1', {
+        'use_pip': False,
+        'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'],
+    }),
+    ('wheel', '0.37.1', {
+        'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl',
+        'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'],
+    }),
+    ('reframe', version, {
+        'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && "
+                          "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && "
+                          "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ",
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'],
+        'checksums': ['f1d38133023b37d01fdee46b2bf472f8fd36bf410d1c909db043b9f9d7df6122'],
+    }),
+]
+
+postinstallcmds = [
+    "cp -a hpctestlib tools tutorials %(installdir)s",
+    "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions",
+    r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe",
+]
+
+sanity_check_paths = {
+    'files': ['bin/reframe',
+              'share/completions/reframe.bash',
+              'share/completions/reframe.fish',
+              'share/completions/reframe.tcsh'],
+    'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials']
+}
+
+sanity_check_commands = ['reframe -V']
+
+sanity_pip_check = True
+
+modextrapaths = {
+    # bootstrap script installs required dependencies to 'external' subdirectory
+    'PYTHONPATH': 'external',
+}
+
+moduleclass = 'devel'

From 24883f825dd505761b42ab6c53faefbeba0b278f Mon Sep 17 00:00:00 2001
From: lukelabrie <lplcleary@gmail.com>
Date: Mon, 8 May 2023 12:14:57 +0200
Subject: [PATCH 496/601] fix broken tarball links for ispc 1.6, 1.10 and 1.12
 easyconfigs

---
 easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb | 6 +++---
 easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb | 6 +++---
 easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb  | 3 ++-
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb
index c83e203d15d..5c8c24efaf6 100644
--- a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb
+++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb
@@ -13,9 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high-
 
 toolchain = SYSTEM
 
-sources = ['ispc-v%(version)s-linux.tar.gz']
-source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')]
-checksums = ['453211ade91c33826f4facb1336114831adbd35196d016e09d589a6ad8699aa3']
+source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/']
+sources = ['ispc-v%(version)sb-linux.tar.gz']
+checksums = ['7fbcf27be161d80a28ab258b3beef3f137a72ac4edc9aa92b1cca044521ff6ca']
 
 sanity_check_paths = {
     'files': ["bin/ispc"],
diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb
index 450f335d81a..cb286e82948 100644
--- a/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb
+++ b/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb
@@ -13,9 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high-
 
 toolchain = SYSTEM
 
-source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')]
-sources = ['ispc-v%(version)s-linux.tar.gz']
-checksums = ['79decaef42bc5433ab30f5879eb91af14473a42e8b51ec727a97f61ee918497e']
+source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/']
+sources = ['ispc-v%(version)sb-linux.tar.gz']
+checksums = ['7a2bdd5fff5c1882639cfbd66bca31dbb68c7177f3013e80b0813a37fe0fdc23']
 
 sanity_check_paths = {
     'files': ["bin/ispc"],
diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb
index b266d99faac..0b7e085e0e3 100644
--- a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb
+++ b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb
@@ -13,8 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high-
 
 toolchain = SYSTEM
 
+source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/']
 sources = ['ispc-v%(version)s-linux.tar.gz']
-source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')]
+checksums = ['67abd92645ead651ced74c4e358313414f5786f0275d975ef4888f168ca342d1']
 
 sanity_check_paths = {
     'files': ["ispc"],

From c799b96a5d1ae72f15bd6ac1a83deedd93930a45 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 May 2023 14:18:19 +0200
Subject: [PATCH 497/601] adding easyconfigs: libharu-2.3.0-GCCcore-11.3.0.eb,
 pftoolsV3-3.2.12-GCCcore-11.3.0.eb

---
 .../l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb | 33 ++++++++++
 .../pftoolsV3-3.2.12-GCCcore-11.3.0.eb        | 60 +++++++++++++++++++
 2 files changed, 93 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..7b7f71ea537
--- /dev/null
+++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'CMakeMake'
+
+name = 'libharu'
+version = '2.3.0'
+
+homepage = 'https://github.com/libharu/libharu/'
+description = """libHaru is a free, cross platform, open source library for generating PDF files."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = [GITHUB_SOURCE]  # https://github.com/libharu/libharu/archive/
+sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))]
+checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2']
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+]
+
+dependencies = [('libpng', '1.6.37')]
+
+parallel = 1
+
+sanity_check_paths = {
+    'files': ['lib/libhpdf.%s' % SHLIB_EXT],
+    'dirs': [
+        'if',
+        'include',
+        'lib',
+    ]
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..51c1ebbe912
--- /dev/null
+++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb
@@ -0,0 +1,60 @@
+easyblock = 'CMakeMake'
+
+name = 'pftoolsV3'
+version = '3.2.12'
+
+homepage = 'https://github.com/sib-swiss/pftools3'
+description = """A suite of tools to build and search generalized profiles (protein and DNA)."""
+software_license = 'LicenseGPLv2'
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/']
+checksums = ['1de33d6444015942afa690d54a103ad5a3d68f416fad63f247c12fa3f71a550c']  # pftools3-3.2.12.tar.gz
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.23.1'),
+    ('make', '4.3'),
+    ('pkgconf', '1.8.0'),
+]
+
+dependencies = [
+    ('libgd', '2.3.3'),
+    ('libharu', '2.3.0'),
+    ('libjpeg-turbo', '2.1.3'),
+    ('libpng', '1.6.37'),
+    ('PCRE2', '10.40'),
+    ('Perl', '5.34.1'),
+    ('zlib', '1.2.12'),
+]
+
+configopts = '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON -DUSE_AFFINITY=OFF'  # Disable affinity for some old architectures
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': [
+        'bin/2ft',
+        'bin/6ft',
+        'bin/htop',
+        'bin/pfdump',
+        'bin/pfscan',
+        'bin/pfscanV3',
+        'bin/pfsearch',
+        'bin/pfsearchV3',
+        'bin/ptof',
+    ],
+    'dirs': [
+        'share/doc',
+        'share/man'
+    ],
+}
+
+sanity_check_commands = [
+    'pfscanV3 --help',
+    'pfsearchV3 --help',
+]
+
+moduleclass = 'bio'

From b46ce7927c8f02d8cd44388e1364d2504307bc29 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Mon, 8 May 2023 18:14:54 +0200
Subject: [PATCH 498/601] adding easyconfigs: GCC-12.3.0.eb, GCCcore-12.3.0.eb,
 binutils-2.40-GCCcore-12.3.0.eb, Bison-3.8.2-GCCcore-12.3.0.eb,
 flex-2.6.4-GCCcore-12.3.0.eb, help2man-1.49.3-GCCcore-12.3.0.eb,
 M4-1.4.19-GCCcore-12.3.0.eb, zlib-1.2.13-GCCcore-12.3.0.eb

---
 .../b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb     | 28 +++++++++
 .../binutils/binutils-2.40-GCCcore-12.3.0.eb  | 31 +++++++++
 .../f/flex/flex-2.6.4-GCCcore-12.3.0.eb       | 34 ++++++++++
 easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb     | 22 +++++++
 .../easyconfigs/g/GCCcore/GCCcore-12.3.0.eb   | 63 +++++++++++++++++++
 .../help2man-1.49.3-GCCcore-12.3.0.eb         | 25 ++++++++
 .../m/M4/M4-1.4.19-GCCcore-12.3.0.eb          | 29 +++++++++
 .../z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb      | 27 ++++++++
 8 files changed, 259 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..36f8bac232a
--- /dev/null
+++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'Bison'
+version = '3.8.2'
+
+homepage = 'https://www.gnu.org/software/bison'
+description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar
+ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb']
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    # use same binutils version that was used when building GCCcore toolchain
+    ('binutils', '2.40', '', SYSTEM),
+]
+
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')],
+    'dirs': [],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..db717c869d8
--- /dev/null
+++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+name = 'binutils'
+version = '2.40'
+
+homepage = 'https://directory.fsf.org/project/binutils/'
+description = "binutils: GNU binary utilities"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956']
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+    # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils
+    ('binutils', version, '', SYSTEM)
+]
+
+dependencies = [
+    # zlib is a runtime dep to avoid that it gets embedded in libbfd.so,
+    # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350
+    ('zlib', '1.2.13'),
+]
+
+# avoid build failure when makeinfo command is not available
+# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345
+buildopts = 'MAKEINFO=true'
+installopts = buildopts
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..a1d5afb9dbd
--- /dev/null
+++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+name = 'flex'
+version = '2.6.4'
+
+homepage = 'https://github.com/westes/flex'
+
+description = """
+ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,
+ sometimes called a tokenizer, is a program which recognizes lexical patterns
+ in text.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995']
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('help2man', '1.49.3'),
+    # use same binutils version that was used when building GCC toolchain
+    ('binutils', '2.40', '', SYSTEM),
+]
+
+dependencies = [
+    ('M4', '1.4.19'),
+]
+
+# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct
+# header, see https://github.com/westes/flex/issues/241
+preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && '
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb
new file mode 100644
index 00000000000..e2701264c4c
--- /dev/null
+++ b/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb
@@ -0,0 +1,22 @@
+easyblock = 'Bundle'
+
+name = 'GCC'
+version = '12.3.0'
+
+homepage = 'https://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = SYSTEM
+
+dependencies = [
+    ('GCCcore', version),
+    # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain)
+    ('binutils', '2.40', '', ('GCCcore', version)),
+]
+
+altroot = 'GCCcore'
+altversion = 'GCCcore'
+
+# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS)
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..c7e0b2a3d08
--- /dev/null
+++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb
@@ -0,0 +1,63 @@
+easyblock = 'EB_GCC'
+
+name = 'GCCcore'
+version = '12.3.0'
+
+homepage = 'https://gcc.gnu.org/'
+description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...)."""
+
+toolchain = SYSTEM
+
+source_urls = [
+    'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s',  # GCC auto-resolving HTTP mirror
+    'https://sourceware.org/pub/gcc/releases/gcc-%(version)s',  # fallback URL for GCC
+    'https://ftpmirror.gnu.org/gnu/gmp',  # idem for GMP
+    'https://ftpmirror.gnu.org/gnu/mpfr',  # idem for MPFR
+    'https://ftpmirror.gnu.org/gnu/mpc',  # idem for MPC
+    'ftp://gcc.gnu.org/pub/gcc/infrastructure/',  # GCC dependencies
+    'https://gcc.gnu.org/pub/gcc/infrastructure/',  # HTTPS mirror for GCC dependencies
+    'https://libisl.sourceforge.io/',  # fallback URL for isl
+    'https://sourceware.org/pub/newlib/',  # for newlib
+    'https://github.com/MentorEmbedded/nvptx-tools/archive',  # for nvptx-tools
+]
+sources = [
+    'gcc-%(version)s.tar.gz',
+    'gmp-6.2.1.tar.bz2',
+    'mpfr-4.1.0.tar.bz2',
+    'mpc-1.2.1.tar.gz',
+    'isl-0.24.tar.bz2',
+    'newlib-4.1.0.tar.gz',
+    {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'},
+]
+patches = [
+    'GCCcore-6.2.0-fix-find-isl.patch',
+    'GCCcore-9.3.0_gmp-c99.patch',
+]
+checksums = [
+    {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'},
+    {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'},
+    {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'},
+    {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'},
+    {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'},
+    {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'},
+    {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'},
+    {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'},
+    {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'},
+]
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    ('binutils', '2.40'),
+]
+
+languages = ['c', 'c++', 'fortran']
+
+withisl = True
+withnvptx = True
+
+# Perl is only required when building with NVPTX support
+if withnvptx:
+    osdependencies = ['perl']
+
+moduleclass = 'compiler'
diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..d3579d82fd8
--- /dev/null
+++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'help2man'
+version = '1.49.3'
+
+homepage = 'https://www.gnu.org/software/help2man/'
+description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_XZ]
+checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f']
+
+builddependencies = [
+    # use same binutils version that was used when building GCC toolchain
+    ('binutils', '2.40', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['bin/help2man'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..9bed7ee958f
--- /dev/null
+++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'M4'
+version = '1.4.19'
+
+homepage = 'https://www.gnu.org/software/m4/m4.html'
+description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible
+  although it has some extensions (for example, handling more than 9 positional parameters to macros).
+ GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70']
+
+# use same binutils version that was used when building GCC toolchain
+builddependencies = [('binutils', '2.40', '', SYSTEM)]
+
+# '-fgnu89-inline' is required to avoid linking errors with older glibc's,
+# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529
+configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline"
+
+sanity_check_paths = {
+    'files': ['bin/m4'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b139a83d3cd
--- /dev/null
+++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'zlib'
+version = '1.2.13'
+
+homepage = 'https://www.zlib.net/'
+description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is,
+ not covered by any patents -- lossless data-compression library for use on virtually any
+ computer hardware and operating system."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://zlib.net/fossils']
+sources = [SOURCELOWER_TAR_GZ]
+# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch']
+checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30']
+
+# use same binutils version that was used when building GCC toolchain
+builddependencies = [('binutils', '2.40', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From 29e0658671e1cb6747a0160dd1ec2574b92c81f7 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Mon, 8 May 2023 18:27:12 +0200
Subject: [PATCH 499/601] GCCcore 12.3.0: update sources

---
 .../easyconfigs/g/GCCcore/GCCcore-12.3.0.eb      | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb
index c7e0b2a3d08..45270c7b7f8 100644
--- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb
@@ -24,10 +24,10 @@ source_urls = [
 sources = [
     'gcc-%(version)s.tar.gz',
     'gmp-6.2.1.tar.bz2',
-    'mpfr-4.1.0.tar.bz2',
-    'mpc-1.2.1.tar.gz',
-    'isl-0.24.tar.bz2',
-    'newlib-4.1.0.tar.gz',
+    'mpfr-4.2.0.tar.bz2',
+    'mpc-1.3.1.tar.gz',
+    'isl-0.26.tar.bz2',
+    'newlib-4.3.0.20230120.tar.gz',
     {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'},
 ]
 patches = [
@@ -37,10 +37,10 @@ patches = [
 checksums = [
     {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'},
     {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'},
-    {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'},
-    {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'},
-    {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'},
-    {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'},
+    {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'},
+    {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'},
+    {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'},
+    {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'},
     {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'},
     {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'},
     {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'},

From 055b6ddef4faad423db1531d833f2a6c491844eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 8 May 2023 20:05:13 +0200
Subject: [PATCH 500/601] adding easyconfigs: bzip2-1.0.8-GCCcore-12.3.0.eb,
 CMake-3.26.3-GCCcore-12.3.0.eb, cURL-8.0.1-GCCcore-12.3.0.eb,
 libarchive-3.6.2-GCCcore-12.3.0.eb, ncurses-6.4-GCCcore-12.3.0.eb,
 XZ-5.4.2-GCCcore-12.3.0.eb

---
 .../b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb     | 27 +++++++++++
 .../c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb    | 30 ++++++++++++
 .../c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb       | 43 +++++++++++++++++
 .../libarchive-3.6.2-GCCcore-12.3.0.eb        | 33 +++++++++++++
 .../n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb   | 47 +++++++++++++++++++
 .../x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb           | 34 ++++++++++++++
 6 files changed, 214 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..cb5b2748e2b
--- /dev/null
+++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb
@@ -0,0 +1,27 @@
+name = 'bzip2'
+version = '1.0.8'
+
+homepage = 'https://sourceware.org/bzip2'
+description = """
+ bzip2 is a freely available, patent free, high-quality data compressor. It
+ typically compresses files to within 10% to 15% of the best available
+ techniques (the PPM family of statistical compressors), whilst being around
+ twice as fast at compression and six times faster at decompression.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://sourceware.org/pub/%(name)s/']
+sources = [SOURCE_TAR_GZ]
+patches = ['bzip2-%(version)s-pkgconfig.patch']
+checksums = [
+    'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269',  # bzip2-1.0.8.tar.gz
+    '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1',  # bzip2-1.0.8-pkgconfig.patch
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..d9b8ac7afaa
--- /dev/null
+++ b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+name = 'CMake'
+version = '3.26.3'
+
+homepage = 'https://www.cmake.org'
+
+description = """
+ CMake, the cross-platform, open-source build system.  CMake is a family of
+ tools designed to build, test and package software.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('ncurses', '6.4'),
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('cURL', '8.0.1'),
+    ('libarchive', '3.6.2'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..18bf937586b
--- /dev/null
+++ b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb
@@ -0,0 +1,43 @@
+easyblock = 'ConfigureMake'
+
+name = 'cURL'
+version = '8.0.1'
+
+homepage = 'https://curl.haxx.se'
+
+description = """
+ libcurl is a free and easy-to-use client-side URL transfer library,
+ supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP,
+ LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP.
+ libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP
+ form based upload, proxies, cookies, user+password authentication (Basic,
+ Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling
+ and more.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://curl.haxx.se/download/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5fd29000a4089934f121eff456101f0a5d09e2a3e89da1d714adf06c4be887cb']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+configopts = '--with-zlib '
+configopts += '--with-ssl=$EBROOTOPENSSL '
+
+modextravars = {'CURL_INCLUDES': '%(installdir)s/include'}
+
+sanity_check_paths = {
+    'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig', 'include/curl'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..3126faae1c5
--- /dev/null
+++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'libarchive'
+version = '3.6.2'
+
+homepage = 'https://www.libarchive.org/'
+
+description = """
+ Multi-format archive and compression library
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://www.libarchive.org/downloads/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('XZ', '5.4.2'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'share/man/man3'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b1731393710
--- /dev/null
+++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb
@@ -0,0 +1,47 @@
+easyblock = 'ConfigureMake'
+
+name = 'ncurses'
+version = '6.4'
+
+homepage = 'https://www.gnu.org/software/ncurses/'
+description = """
+ The Ncurses (new curses) library is a free software emulation of curses in
+ System V Release 4.0, and more. It uses Terminfo format, supports pads and
+ color and multiple highlights and forms characters and function-key mapping,
+ and has all the other SYSV-curses enhancements over BSD Curses.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159']
+
+builddependencies = [('binutils', '2.40')]
+
+local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms "
+configopts = [
+    # build ncurses: serial build in default paths with shared libraries
+    local_common_configopts,
+    # build ncursesw: serial with UTF-8
+    local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/",
+]
+
+# Symlink libtinfo to libncurses
+# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically
+postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done']
+
+_target_suffix = ['', 'w']  # '': ncurses, 'w': ncursesw
+_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]]
+_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config",
+                                     "reset", "tabs", "tic", "toe", "tput", "tset"]] +
+             ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] +
+             ['lib/libncurses++%s.a' % x for x in _target_suffix],
+    'dirs': ['include', 'include/ncursesw'],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..ade6916dd58
--- /dev/null
+++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'XZ'
+version = '5.4.2'
+
+homepage = 'https://tukaani.org/xz/'
+description = "xz: XZ utilities"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://tukaani.org/xz/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['aa49909cbd9028c4666a35fa4975f9a6203ed98154fbb8223ee43ef9ceee97c3']
+
+builddependencies = [
+    # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ)
+    ('gettext', '0.21.1', '', SYSTEM),
+    ('binutils', '2.40'),
+]
+
+# may become useful in non-x86 archs
+# configopts = ' --disable-assembler '
+
+sanity_check_paths = {
+    'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "xz --help",
+    "unxz --help",
+]
+
+moduleclass = 'tools'

From 1baef1234c448b2a0fccebc3c2ef5682074b6ae1 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 9 May 2023 00:10:18 +0200
Subject: [PATCH 501/601] adding easyconfigs:
 dask-labextension-6.0.0-foss-2022a.eb

---
 .../dask-labextension-6.0.0-foss-2022a.eb     | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb
new file mode 100644
index 00000000000..584ac781fbc
--- /dev/null
+++ b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb
@@ -0,0 +1,44 @@
+easyblock = 'PythonBundle'
+
+name = 'dask-labextension'
+version = '6.0.0'
+
+homepage = 'https://github.com/dask/dask-labextension'
+description = """This package provides a JupyterLab extension to manage Dask clusters, as well
+as embed Dask's dashboard plots directly into JupyterLab panes."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('nodejs', '16.15.1'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('JupyterLab', '3.5.0'),
+    ('jupyter-server-proxy', '3.2.2'),
+    ('dask', '2022.10.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('dask_labextension', version, {
+        'checksums': ['516d1faccd0b172d07f794250a5c3427b082d70954ebe8d3f9c92dc08cb79f7e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/dask_labextension', 'etc/jupyter', 'share/jupyter'],
+}
+
+modextrapaths = {
+    'JUPYTER_PATH': 'share/jupyter',
+    'JUPYTER_CONFIG_PATH': 'etc/jupyter',
+}
+
+moduleclass = 'tools'

From 4db0c8d618eeece87cf6e2e9d19b6f7f867977df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 9 May 2023 10:30:24 +0200
Subject: [PATCH 502/601] Also update MPFR & co in GCCcore 13.1.0

---
 .../easyconfigs/g/GCCcore/GCCcore-13.1.0.eb      | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb
index 3493e06b275..5805f7d8a96 100644
--- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb
+++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb
@@ -24,10 +24,10 @@ source_urls = [
 sources = [
     'gcc-%(version)s.tar.gz',
     'gmp-6.2.1.tar.bz2',
-    'mpfr-4.1.0.tar.bz2',
-    'mpc-1.2.1.tar.gz',
-    'isl-0.24.tar.bz2',
-    'newlib-4.1.0.tar.gz',
+    'mpfr-4.2.0.tar.bz2',
+    'mpc-1.3.1.tar.gz',
+    'isl-0.26.tar.bz2',
+    'newlib-4.3.0.20230120.tar.gz',
     {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'},
 ]
 patches = [
@@ -37,10 +37,10 @@ patches = [
 checksums = [
     {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'},
     {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'},
-    {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'},
-    {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'},
-    {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'},
-    {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'},
+    {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'},
+    {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'},
+    {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'},
+    {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'},
     {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'},
     {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'},
     {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'},

From 3ee5447b983bcde19c15c1fc1abc18adebfa9e22 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 9 May 2023 18:47:06 +0200
Subject: [PATCH 503/601] Rename opencv egg info, also add pkg info file
 generation

---
 .../o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb  | 3 ++-
 .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb  | 5 +++--
 ...ontrib-python.egg-info => opencv_contrib_python.egg-info} | 0
 3 files changed, 5 insertions(+), 3 deletions(-)
 rename easybuild/easyconfigs/o/OpenCV/{opencv-contrib-python.egg-info => opencv_contrib_python.egg-info} (100%)

diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
index 0edcf1239a6..31c84ed6b6e 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
@@ -38,7 +38,7 @@ checksums = [
     {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'},
     {'ippicv_2020_lnx_intel64_20191018_general.tgz':
      '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'},
-    {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'},
+    {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'},
 ]
 
 builddependencies = [
@@ -71,6 +71,7 @@ dependencies = [
 # ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861
 configopts = " ".join([
     "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules",
+    "-DOPENCV_GENERATE_PKGCONFIG=ON",
     "-DFREETYPE_FOUND=ON",
     "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/",
     "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so",
diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
index 6373a8db53e..62d6005f265 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
@@ -37,7 +37,7 @@ checksums = [
     {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'},
     {'ippicv_2020_lnx_intel64_20191018_general.tgz':
      '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'},
-    {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'},
+    {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'},
 ]
 
 builddependencies = [
@@ -68,6 +68,7 @@ dependencies = [
 # ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861
 configopts = " ".join([
     "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules",
+    "-DOPENCV_GENERATE_PKGCONFIG=ON",
     "-DFREETYPE_FOUND=ON",
     "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/",
     "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so",
@@ -98,7 +99,7 @@ local_contrib_libs = [
 ]
 
 sanity_check_paths = {
-    'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs],
+    'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs],
     'dirs': [],
 }
 
diff --git a/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info b/easybuild/easyconfigs/o/OpenCV/opencv_contrib_python.egg-info
similarity index 100%
rename from easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info
rename to easybuild/easyconfigs/o/OpenCV/opencv_contrib_python.egg-info

From 7aa8e3dae5396387b4ef113b61e9014a0c60be26 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 9 May 2023 19:33:46 +0200
Subject: [PATCH 504/601] Fix patch filename

---
 .../o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb     | 2 +-
 .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
index 31c84ed6b6e..bb75837b40e 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
@@ -32,7 +32,7 @@ sources = [
         'extract_cmd': 'cp %s %(builddir)s'
     },
 ]
-patches = [('opencv-contrib-python.egg-info', '..')]
+patches = [('opencv_contrib_python.egg-info', '..')]
 checksums = [
     {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'},
     {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'},
diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
index 62d6005f265..b2fd1d672bc 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
@@ -31,7 +31,7 @@ sources = [
         'extract_cmd': 'cp %s %(builddir)s'
     },
 ]
-patches = [('opencv-contrib-python.egg-info', '..')]
+patches = [('opencv_contrib_python.egg-info', '..')]
 checksums = [
     {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'},
     {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'},

From c2d40724a619e995e0d65675681bbe4ae23e5354 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 9 May 2023 11:38:10 -0700
Subject: [PATCH 505/601] update version, add ABSL replace PR #17862

---
 .../protobuf/protobuf-22.4-GCCcore-12.2.0.eb  | 39 +++++++++++++++++++
 .../protobuf-22.4_linking-error.patch         | 37 ++++++++++++++++++
 2 files changed, 76 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb
 create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch

diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..3c78b97f75d
--- /dev/null
+++ b/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'CMakeMake'
+
+name = 'protobuf'
+version = '22.4'
+
+homepage = 'https://github.com/protocolbuffers/protobuf'
+description = """Protocol Buffers (a.k.a., protobuf) are Google's 
+language-neutral, platform-neutral, extensible mechanism for 
+serializing structured data."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+patches = ['protobuf-22.4_linking-error.patch']
+checksums = [
+    'def8683aafc1ebaddbc777da252dfdc8e324a197757e3bfcd8b4de90d4b8cf6a',  # v22.4.tar.gz
+    '6c514ee1854fe40855a2db4a1cd197f9a30ec5be6d7c50932d4eb061788a151c',  # protobuf-22.4_linking-error.patch
+]
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+srcdir = 'cmake'
+
+configopts = "-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER='package'"
+
+dependencies = [
+    ('Abseil', '20230125.2'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch b/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch
new file mode 100644
index 00000000000..0e83d971c78
--- /dev/null
+++ b/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch
@@ -0,0 +1,37 @@
+# https://github.com/protocolbuffers/protobuf/pull/11032
+diff -ruN protobuf-22.4.orig/src/libprotobuf-lite.map protobuf-22.4/src/libprotobuf-lite.map
+--- protobuf-22.4.orig/src/libprotobuf-lite.map	2023-05-03 10:23:58.000000000 -0700
++++ protobuf-22.4/src/libprotobuf-lite.map	2023-05-09 10:53:18.018860000 -0700
+@@ -3,6 +3,8 @@
+     extern "C++" {
+       *google*;
+     };
++  scc_info_*;
++  descriptor_table_*;
+ 
+   local:
+     *;
+diff -ruN protobuf-22.4.orig/src/libprotobuf.map protobuf-22.4/src/libprotobuf.map
+--- protobuf-22.4.orig/src/libprotobuf.map	2023-05-03 10:23:58.000000000 -0700
++++ protobuf-22.4/src/libprotobuf.map	2023-05-09 10:53:56.908337000 -0700
+@@ -3,6 +3,8 @@
+     extern "C++" {
+       *google*;
+     };
++  scc_info_*;
++  descriptor_table_*;
+ 
+   local:
+     *;
+diff -ruN protobuf-22.4.orig/src/libprotoc.map protobuf-22.4/src/libprotoc.map
+--- protobuf-22.4.orig/src/libprotoc.map	2023-05-03 10:23:58.000000000 -0700
++++ protobuf-22.4/src/libprotoc.map	2023-05-09 10:54:46.728401000 -0700
+@@ -3,6 +3,8 @@
+     extern "C++" {
+       *google*;
+     };
++  scc_info_*;
++  descriptor_table_*;
+ 
+   local:
+     *;

From 2523a40b4847bba44dddf635dbd4d7a1bb9298d0 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 9 May 2023 12:01:25 -0700
Subject: [PATCH 506/601] more protobuf

---
 .../protobuf-python-4.23.0-GCCcore-12.2.0.eb  | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..957af949a32
--- /dev/null
+++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'PythonPackage'
+
+name = 'protobuf-python'
+version = '4.23.0'
+
+homepage = 'https://github.com/google/protobuf/'
+description = """Python Protocol Buffers runtime library."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://pypi.python.org/packages/source/p/protobuf']
+sources = ['protobuf-%(version)s.tar.gz']
+checksums = ['5f1eba1da2a2f3f7df469fccddef3cc060b8a16cfe3cc65961ad36b4dbcf59c5']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('protobuf', '22.4')
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+# Make sure protobuf is installed as a regular folder or it will not be found if
+# other google packages are installed in other site-packages folders
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'],
+}
+
+options = {'modulename': 'google.protobuf'}
+
+moduleclass = 'devel'

From 29245ce43891922da478f9269442dc0ea2ef2061 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 9 May 2023 21:35:37 +0200
Subject: [PATCH 507/601] install dask-labextension v6.0.0 from wheel

---
 .../dask-labextension-6.0.0-foss-2022a.eb                 | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb
index 584ac781fbc..54f6a5881f7 100644
--- a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb
@@ -9,11 +9,6 @@ as embed Dask's dashboard plots directly into JupyterLab panes."""
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
-builddependencies = [
-    ('binutils', '2.38'),
-    ('nodejs', '16.15.1'),
-]
-
 dependencies = [
     ('Python', '3.10.4'),
     ('JupyterLab', '3.5.0'),
@@ -25,7 +20,8 @@ use_pip = True
 
 exts_list = [
     ('dask_labextension', version, {
-        'checksums': ['516d1faccd0b172d07f794250a5c3427b082d70954ebe8d3f9c92dc08cb79f7e'],
+        'sources': ['%(name)s-%(version)s-py3-none-any.whl'],
+        'checksums': ['6b9e6a66fec891d6533314b03a57e121eb9822aaf98c94139c913e7c30212002'],
     }),
 ]
 

From 6ff2c1f432760095ee24c964a3b5818e499a73a3 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 9 May 2023 22:38:37 +0200
Subject: [PATCH 508/601] add dependency on PycURL to
 JupyterHub-3.0.0-GCCcore-11.3.0.eb

---
 .../JupyterHub-3.0.0-GCCcore-11.3.0.eb        |  3 +-
 .../p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb  | 28 +++++++++++++++++++
 2 files changed, 30 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb
index 9f427a4cb20..4addecfb2d6 100644
--- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb
@@ -19,7 +19,8 @@ dependencies = [
     ('Mako', '1.2.0'),
     ('configurable-http-proxy', '4.5.3'),
     ('OpenSSL', '1.1', '', SYSTEM),
-    ('jupyter-server-proxy', '3.2.2')  # This is optional, but commonly used together
+    ('jupyter-server-proxy', '3.2.2'),  # optional, but commonly used together
+    ('PycURL', '7.45.2'),  # optional, recommended with large number of users
 ]
 
 use_pip = True
diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..721db47c2b2
--- /dev/null
+++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb
@@ -0,0 +1,28 @@
+# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham.
+easyblock = 'PythonPackage'
+
+name = 'PycURL'
+version = '7.45.2'
+
+homepage = "http://pycurl.io/"
+description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL
+ from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of
+ features."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('cURL', '7.83.0'),
+]
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca']
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+moduleclass = 'tools'

From 4035b4ee11cb1dc9e2c6398ce837bd52d5fa3dba Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 9 May 2023 22:42:51 +0200
Subject: [PATCH 509/601] adding easyconfigs:
 jupyterlmod-4.0.3-GCCcore-11.3.0.eb

---
 .../jupyterlmod-4.0.3-GCCcore-11.3.0.eb       | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..741b452e01a
--- /dev/null
+++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'jupyterlmod'
+version = '4.0.3'
+
+# This easyconfig installs the notebook and lab extension of Jupyter Lmod
+
+homepage = 'https://github.com/cmd-ntrf/jupyter-lmod'
+description = """Jupyter interactive notebook server extension that allows user to interact with
+environment modules before launching kernels. The extension use Lmod's Python
+interface to accomplish module related task like loading, unloading, saving
+collection, etc."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('IPython', '8.5.0'),
+    ('jupyter-server', '1.21.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'sources': ['%(name)s-%(version)s-py3-none-any.whl'],
+        'checksums': ['9939bd7927c2c347f9884247bac58018ca44d56184c5f29e9d704a9b3a09a299'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'],
+}
+
+modextrapaths = {
+    'JUPYTER_PATH': 'share/jupyter',
+    'JUPYTER_CONFIG_PATH': 'etc/jupyter',
+}
+
+moduleclass = 'tools'

From 945ee02a75df9b36649d0e658e4333d65b80ad88 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 9 May 2023 17:49:27 -0700
Subject: [PATCH 510/601] bump version

---
 .../protobuf-python-4.23.0-GCCcore-12.2.0.eb  |  2 +-
 .../protobuf/protobuf-22.4-GCCcore-12.2.0.eb  | 39 -------------------
 .../protobuf-22.4_linking-error.patch         | 37 ------------------
 3 files changed, 1 insertion(+), 77 deletions(-)
 delete mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb
 delete mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch

diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb
index 957af949a32..5a00b1b6fdd 100644
--- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb
+++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb
@@ -16,7 +16,7 @@ builddependencies = [('binutils', '2.39')]
 
 dependencies = [
     ('Python', '3.10.8'),
-    ('protobuf', '22.4')
+    ('protobuf', '23.0')
 ]
 
 download_dep_fail = True
diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb
deleted file mode 100644
index 3c78b97f75d..00000000000
--- a/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb
+++ /dev/null
@@ -1,39 +0,0 @@
-easyblock = 'CMakeMake'
-
-name = 'protobuf'
-version = '22.4'
-
-homepage = 'https://github.com/protocolbuffers/protobuf'
-description = """Protocol Buffers (a.k.a., protobuf) are Google's 
-language-neutral, platform-neutral, extensible mechanism for 
-serializing structured data."""
-
-toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
-
-source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/']
-sources = ['v%(version)s.tar.gz']
-patches = ['protobuf-22.4_linking-error.patch']
-checksums = [
-    'def8683aafc1ebaddbc777da252dfdc8e324a197757e3bfcd8b4de90d4b8cf6a',  # v22.4.tar.gz
-    '6c514ee1854fe40855a2db4a1cd197f9a30ec5be6d7c50932d4eb061788a151c',  # protobuf-22.4_linking-error.patch
-]
-
-builddependencies = [
-    ('binutils', '2.39'),
-    ('CMake', '3.24.3'),
-]
-
-srcdir = 'cmake'
-
-configopts = "-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER='package'"
-
-dependencies = [
-    ('Abseil', '20230125.2'),
-]
-
-sanity_check_paths = {
-    'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT],
-    'dirs': [],
-}
-
-moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch b/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch
deleted file mode 100644
index 0e83d971c78..00000000000
--- a/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-# https://github.com/protocolbuffers/protobuf/pull/11032
-diff -ruN protobuf-22.4.orig/src/libprotobuf-lite.map protobuf-22.4/src/libprotobuf-lite.map
---- protobuf-22.4.orig/src/libprotobuf-lite.map	2023-05-03 10:23:58.000000000 -0700
-+++ protobuf-22.4/src/libprotobuf-lite.map	2023-05-09 10:53:18.018860000 -0700
-@@ -3,6 +3,8 @@
-     extern "C++" {
-       *google*;
-     };
-+  scc_info_*;
-+  descriptor_table_*;
- 
-   local:
-     *;
-diff -ruN protobuf-22.4.orig/src/libprotobuf.map protobuf-22.4/src/libprotobuf.map
---- protobuf-22.4.orig/src/libprotobuf.map	2023-05-03 10:23:58.000000000 -0700
-+++ protobuf-22.4/src/libprotobuf.map	2023-05-09 10:53:56.908337000 -0700
-@@ -3,6 +3,8 @@
-     extern "C++" {
-       *google*;
-     };
-+  scc_info_*;
-+  descriptor_table_*;
- 
-   local:
-     *;
-diff -ruN protobuf-22.4.orig/src/libprotoc.map protobuf-22.4/src/libprotoc.map
---- protobuf-22.4.orig/src/libprotoc.map	2023-05-03 10:23:58.000000000 -0700
-+++ protobuf-22.4/src/libprotoc.map	2023-05-09 10:54:46.728401000 -0700
-@@ -3,6 +3,8 @@
-     extern "C++" {
-       *google*;
-     };
-+  scc_info_*;
-+  descriptor_table_*;
- 
-   local:
-     *;

From 8b26880d863a8aacefd390e40994b76553748d86 Mon Sep 17 00:00:00 2001
From: fizwit <john@fuzzdog.com>
Date: Tue, 9 May 2023 17:50:47 -0700
Subject: [PATCH 511/601] bump version

---
 .../protobuf/protobuf-23.0-GCCcore-12.2.0.eb  | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..962f6810124
--- /dev/null
+++ b/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'CMakeMake'
+
+name = 'protobuf'
+version = '23.0'
+
+homepage = 'https://github.com/protocolbuffers/protobuf'
+description = """Protocol Buffers (a.k.a., protobuf) are Google's 
+language-neutral, platform-neutral, extensible mechanism for 
+serializing structured data."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['b8faf8487cc364e5c2b47a9abd77512bc79a6389ea45392ca938ba7617eae877']
+
+builddependencies = [
+    ('binutils', '2.39'),
+    ('CMake', '3.24.3'),
+]
+
+srcdir = '.'
+
+configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" '
+
+dependencies = [
+    ('Abseil', '20230125.2'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From a1d2ff4ef82f032f247a152716b7beeeec128be1 Mon Sep 17 00:00:00 2001
From: Adam Huffman <verdurin@users.noreply.github.com>
Date: Wed, 10 May 2023 09:22:16 +0100
Subject: [PATCH 512/601] Update jupyterlmod-4.0.3-GCCcore-11.3.0.eb

Minor grammar fixes to description
---
 .../j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb     | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb
index 741b452e01a..552befac655 100644
--- a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb
@@ -6,10 +6,10 @@ version = '4.0.3'
 # This easyconfig installs the notebook and lab extension of Jupyter Lmod
 
 homepage = 'https://github.com/cmd-ntrf/jupyter-lmod'
-description = """Jupyter interactive notebook server extension that allows user to interact with
-environment modules before launching kernels. The extension use Lmod's Python
-interface to accomplish module related task like loading, unloading, saving
-collection, etc."""
+description = """Jupyter interactive notebook server extension that allows users to interact with
+environment modules before launching kernels. The extension uses Lmod's Python
+interface to accomplish module-related tasks like loading, unloading, saving
+collections, etc."""
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 

From 0f4e75499e8fbd0eec4b665c5c5a4928aa5ec09e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 10 May 2023 10:49:54 +0200
Subject: [PATCH 513/601] Fix another incorrect filename path

---
 .../o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb   | 4 ++--
 .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
index bb75837b40e..4ca1c26a38c 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb
@@ -87,8 +87,8 @@ configopts = " ".join([
 ])
 
 # Install a egg-info file so it is more python friendly
-local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info'
-local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info'
+local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info'
 postinstallcmds = [
     'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
 ]
diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
index b2fd1d672bc..f71431e0f08 100644
--- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
+++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb
@@ -83,8 +83,8 @@ configopts = " ".join([
 ])
 
 # Install a egg-info file so it is more python friendly
-local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info'
-local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info'
+local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info'
+local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info'
 postinstallcmds = [
     'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest),
 ]

From 2251af9b2a4c8a4d80afee1ab80589dd03b0fbf5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 10 May 2023 11:19:50 +0200
Subject: [PATCH 514/601] adding easyconfigs:
 L_RNA_scaffolder-20190530-GCC-11.3.0.eb

---
 .../L_RNA_scaffolder-20190530-GCC-11.3.0.eb   | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb
new file mode 100644
index 00000000000..59d93ffd865
--- /dev/null
+++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'Tarball'
+
+name = 'L_RNA_scaffolder'
+local_commit = '98f19e3'
+version = '20190530'
+
+homepage = 'https://github.com/CAFS-bioinformatics/L_RNA_scaffolder'
+description = "L_RNA_scaffolder is a genome scaffolding tool with long trancriptome reads"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/CAFS-bioinformatics/L_RNA_scaffolder/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['ef4c5bf3511e9947bdb33201bdcaf1ff779ca315a2139f73bb549fb6bfc05f5a']
+
+dependencies = [
+    ('BioPerl', '1.7.8'),
+]
+
+fix_perl_shebang_for = ['*.pl']
+
+postinstallcmds = ["chmod a+x %(installdir)s/L_RNA_scaffolder.sh"]
+
+sanity_check_paths = {
+    'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency',
+              'delete_block', 'delete_linker', 'delete_same_fragment', 'filter_scaffold.pl',
+              'find_end_node', 'find_reliable_connection', 'find_start_node', 'form_block',
+              'form_path.pl', 'generate_scaffold.pl', 'generate_unscaffold.pl', 'L_RNA_scaffolder.sh', 'link_block',
+              'order', 'overlap', 'route.pl', 'search_guider', 'select_nodes'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["L_RNA_scaffolder.sh -? | grep '^Usage: sh L_RNA_scaffolder.sh'"]
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'bio'

From bd7583cea7d004676c98fd340a862f2d0f241704 Mon Sep 17 00:00:00 2001
From: Thomas Hayward-Schneider <thomas.hayward@ipp.mpg.de>
Date: Wed, 10 May 2023 16:45:57 +0200
Subject: [PATCH 515/601] texlive: add historical repo paths to install cmd

* see discussion in https://github.com/easybuilders/easybuild-easyconfigs/issues/17871
---
 .../t/texlive/texlive-20200406-GCCcore-8.3.0.eb            | 7 ++++++-
 .../easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb   | 6 ++++--
 .../easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb   | 6 ++++--
 .../easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb   | 2 ++
 4 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb
index 7c74e626642..4e8bf18c2f4 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb
@@ -4,6 +4,7 @@ easyblock = 'Tarball'
 
 name = 'texlive'
 version = '20200406'
+local_version_year = version[:4]
 
 homepage = 'https://tug.org'
 description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript
@@ -13,7 +14,10 @@ description = """TeX is a typesetting language. Instead of visually formatting y
 
 toolchain = {'name': 'GCCcore', 'version': '8.3.0'}
 
-source_urls = ['ftp://tug.org/texlive/historic/2020/']
+source_urls = [
+    'ftp://tug.org/texlive/historic/%s/' % local_version_year,
+    'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year,
+]
 sources = [
     {
         'download_filename': 'install-tl-unx.tar.gz',
@@ -41,6 +45,7 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
+    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {
diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb
index 9809666eaa4..86aa9943d93 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb
@@ -4,6 +4,7 @@ easyblock = 'Tarball'
 
 name = 'texlive'
 version = '20210324'
+local_version_year = version[:4]
 
 homepage = 'https://tug.org'
 description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript
@@ -14,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y
 toolchain = {'name': 'GCC', 'version': '10.3.0'}
 
 source_urls = [
-    'ftp://tug.org/texlive/historic/2021/',
-    'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/',
+    'ftp://tug.org/texlive/historic/%s/' % local_version_year,
+    'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year,
 ]
 sources = [
     {
@@ -44,6 +45,7 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
+    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {
diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb
index b00d0026d53..7f55d4478f9 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb
@@ -4,6 +4,7 @@ easyblock = 'Tarball'
 
 name = 'texlive'
 version = '20210324'
+local_version_year = version[:4]
 
 homepage = 'https://tug.org'
 description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript
@@ -14,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y
 toolchain = {'name': 'GCC', 'version': '11.2.0'}
 
 source_urls = [
-    'ftp://tug.org/texlive/historic/2021/',
-    'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/',
+    'ftp://tug.org/texlive/historic/%s/' % local_version_year,
+    'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year,
 ]
 sources = [
     {
@@ -44,6 +45,7 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
+    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {
diff --git a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb
index d249ac772bf..014f57053c8 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb
@@ -4,6 +4,7 @@ easyblock = 'Tarball'
 
 name = 'texlive'
 version = '20220321'
+local_version_year = version[:4]
 
 homepage = 'https://tug.org'
 description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript
@@ -44,6 +45,7 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
+    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {

From 809c2b68617dec8974cb56394b8f6ed6f28aed99 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 10 May 2023 18:30:35 +0200
Subject: [PATCH 516/601] Remove dup checksum

---
 .../easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb      | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb
index d24ee4f3b3c..c11baed2797 100644
--- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb
@@ -164,7 +164,6 @@ crates = [
 source_urls = ['https://github.com/pjedge/longshot/archive']
 sources = ['v%(version)s.tar.gz']
 checksums = [
-    {'v0.4.5.tar.gz': '7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad'},
     {'v0.4.5.tar.gz': '7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad'},
     {'addr2line-0.19.0.tar.gz': 'a76fd60b23679b7d19bd066031410fb7e458ccc5e958eb5c325888ce4baedc97'},
     {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},

From 10412a687581c2fb22697570155851c2e764378e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 10 May 2023 18:34:30 +0200
Subject: [PATCH 517/601] Add checksums for all crates

---
 .../bamtofastq-1.4.0-GCCcore-10.3.0.eb        | 170 +++++++++++++++++-
 1 file changed, 169 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
index 2daaefe9ffe..f882fbbd838 100644
--- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb
@@ -178,7 +178,175 @@ crates = [
 ]
 source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags']
 sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
-checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed']
+checksums = [
+    {'bamtofastq-1.4.0.tar.gz': 'b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'},
+    {'anyhow-1.0.44.tar.gz': '61604a8f862e1d5c3229fdd78f8b02c68dcf73a4c4b05fd636d12240aaa242c1'},
+    {'backtrace-0.3.61.tar.gz': 'e7a905d892734eea339e896738c14b9afce22b5318f64b951e70bf3844419b01'},
+    {'addr2line-0.16.0.tar.gz': '3e61f2b7f93d2c7d2b08263acaa4a363b3e276806c68af6134c44f523bf1aacd'},
+    {'gimli-0.25.0.tar.gz': 'f0a01e0497841a3b2db4f8afa483cce65f7e96a3498bd6c541734792aeac8fe7'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'miniz_oxide-0.4.4.tar.gz': 'a92518e98c078586bc6c934028adcca4c92a53d6a958196de835170a01d84e4b'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'autocfg-1.0.1.tar.gz': 'cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a'},
+    {'object-0.26.2.tar.gz': '39f37e50073ccad23b6d09bcb5b263f4e76d3bb6038e4a3c08e52162ffa8abc2'},
+    {'memchr-2.4.1.tar.gz': '308cc39be01b73d0d18f82a0e7b2a3df85245f84af96fdddc5d202d27e47b86a'},
+    {'rustc-demangle-0.1.21.tar.gz': '7ef03e0a2b150c7a90d01faf6254c9c48a41e95fb2a8c2ac1c6f0d2b9aefc342'},
+    {'cc-1.0.71.tar.gz': '79c2681d6594606957bbb8631c4b90a7fcaaa72cdb714743a437b156d6a7eedd'},
+    {'jobserver-0.1.24.tar.gz': 'af25a77299a7f711a01975c35a6a424eb6862092cc2d6c72c4ed6cbc56dfc1fa'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'backtrace-0.3.61.tar.gz': 'e7a905d892734eea339e896738c14b9afce22b5318f64b951e70bf3844419b01'},
+    {'bincode-1.3.3.tar.gz': 'b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad'},
+    {'serde-1.0.130.tar.gz': 'f12d06de37cf59146fbdecab66aa99f9fe4f78722e3607577a5375d66bd0c913'},
+    {'serde_derive-1.0.130.tar.gz': 'd7bc1a1ab1961464eae040d96713baa5a724a8152c1222492465b54322ec508b'},
+    {'proc-macro2-1.0.29.tar.gz': 'b9f5105d4fdaab20335ca9565e106a5d9b82b6219b5ba735731124ac6711d23d'},
+    {'unicode-xid-0.2.2.tar.gz': '8ccb82d61f80a663efe1f787a51b16b5a51e3314d6ac365b08639f52387b33f3'},
+    {'quote-1.0.10.tar.gz': '38bc8cc6a5f2e3655e0899c1b848643b2562f853f114bfec7be120678e3ace05'},
+    {'proc-macro2-1.0.29.tar.gz': 'b9f5105d4fdaab20335ca9565e106a5d9b82b6219b5ba735731124ac6711d23d'},
+    {'syn-1.0.80.tar.gz': 'd010a1623fbd906d51d650a9916aaefc05ffa0e4053ff7fe601167f3e715d194'},
+    {'proc-macro2-1.0.29.tar.gz': 'b9f5105d4fdaab20335ca9565e106a5d9b82b6219b5ba735731124ac6711d23d'},
+    {'quote-1.0.10.tar.gz': '38bc8cc6a5f2e3655e0899c1b848643b2562f853f114bfec7be120678e3ace05'},
+    {'unicode-xid-0.2.2.tar.gz': '8ccb82d61f80a663efe1f787a51b16b5a51e3314d6ac365b08639f52387b33f3'},
+    {'csv-1.1.6.tar.gz': '22813a6dc45b335f9bade10bf7271dc477e81113e89eb251a0bc2a8a81c536e1'},
+    {'bstr-0.2.17.tar.gz': 'ba3569f383e8f1598449f1a423e72e99569137b47740b1da11ef19af3d5c3223'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'memchr-2.4.1.tar.gz': '308cc39be01b73d0d18f82a0e7b2a3df85245f84af96fdddc5d202d27e47b86a'},
+    {'regex-automata-0.1.10.tar.gz': '6c230d73fb8d8c1b9c0b3135c5142a8acee3a0558fb8db5cf1cb65f8d7862132'},
+    {'serde-1.0.130.tar.gz': 'f12d06de37cf59146fbdecab66aa99f9fe4f78722e3607577a5375d66bd0c913'},
+    {'csv-core-0.1.10.tar.gz': '2b2466559f260f48ad25fe6317b3c8dac77b5bdb5763ac7d9d6103530663bc90'},
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+    {'ieee754-0.2.6.tar.gz': '9007da9cacbd3e6343da136e98b0d2df013f553d35bdec8b518f07bea768e19c'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'linear-map-1.2.0.tar.gz': 'bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee'},
+    {'newtype_derive-0.1.6.tar.gz': 'ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec'},
+    {'rustc_version-0.1.7.tar.gz': 'c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084'},
+    {'semver-0.1.20.tar.gz': 'd4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac'},
+    {'regex-1.5.4.tar.gz': 'd07a8629359eb56f1e2fb1652bb04212c072a87ba68546a04065d525673ac461'},
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+    {'idna-0.2.3.tar.gz': '418a0a6fab821475f634efe3ccc45c013f742efe03d853e8d3355d5cb850ecf8'},
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+    {'unicode-bidi-0.3.7.tar.gz': '1a01404663e3db436ed2746d9fefef640d868edae3cceb81c3b8d5732fda678f'},
+    {'unicode-normalization-0.1.19.tar.gz': 'd54590932941a9e9266f0832deed84ebe1bf2e4c9e4a3554d393d18f5e854bf9'},
+    {'tinyvec-1.5.0.tar.gz': 'f83b2a3d4d9091d0abd7eba4dc2710b1718583bd4d8992e2190720ea38f391f7'},
+    {'tinyvec_macros-0.1.0.tar.gz': 'cda74da7e1a664f795bb1f8a87ec406fb89a02522cf6e50620d016add6dbbf5c'},
+    {'matches-0.1.9.tar.gz': 'a3e378b66a060d48947b590737b30a1be76706c8dd7b8ba0f2fe3989c68a853f'},
+    {'percent-encoding-2.1.0.tar.gz': 'd4fd5641d01c8f18a23da7b6fe29298ff4b55afcccdf78973b24cf3175fee32e'},
+    {'serde-1.0.130.tar.gz': 'f12d06de37cf59146fbdecab66aa99f9fe4f78722e3607577a5375d66bd0c913'},
+    {'serde_bytes-0.11.5.tar.gz': '16ae07dd2f88a366f15bd0632ba725227018c69a1c8550a927324f8eb8368bb9'},
+    {'serde-1.0.130.tar.gz': 'f12d06de37cf59146fbdecab66aa99f9fe4f78722e3607577a5375d66bd0c913'},
+    {'serde_derive-1.0.130.tar.gz': 'd7bc1a1ab1961464eae040d96713baa5a724a8152c1222492465b54322ec508b'},
+    {'shardio-0.8.1.tar.gz': 'd8496139ffe2b2dafa0ecaec339bb6d6a760c70781d1d5977e33de638ce80ca2'},
+    {'anyhow-1.0.44.tar.gz': '61604a8f862e1d5c3229fdd78f8b02c68dcf73a4c4b05fd636d12240aaa242c1'},
+    {'bincode-1.3.3.tar.gz': 'b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad'},
+    {'byteorder-1.4.3.tar.gz': '14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610'},
+    {'crossbeam-channel-0.5.1.tar.gz': '06ed27e177f16d65f0f0c22a213e17c696ace5dd64b14258b52f9417ccb52db4'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'crossbeam-utils-0.8.5.tar.gz': 'd82cfc11ce7f2c3faef78d8a684447b40d503d9681acebed6cb728d45940c4db'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
+    {'log-0.4.14.tar.gz': '51b9bbe6c47d51fc3e1a9b945965946b4c44142ab8792c50835a980d362c2710'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'lz4-1.23.2.tar.gz': 'aac20ed6991e01bf6a2e68cc73df2b389707403662a8ba89f68511fb340f724c'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'lz4-sys-1.9.2.tar.gz': 'dca79aa95d8b3226213ad454d328369853be3a1382d89532a854f4d69640acae'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'cc-1.0.71.tar.gz': '79c2681d6594606957bbb8631c4b90a7fcaaa72cdb714743a437b156d6a7eedd'},
+    {'min-max-heap-1.3.0.tar.gz': '2687e6cf9c00f48e9284cf9fd15f2ef341d03cc7743abf9df4c5f07fdee50b18'},
+    {'serde-1.0.130.tar.gz': 'f12d06de37cf59146fbdecab66aa99f9fe4f78722e3607577a5375d66bd0c913'},
+    {'tempfile-3.2.0.tar.gz': 'dac1c663cfc93810f88aed9b8941d48cabf856a1b111c29a40439018d870eb22'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'rand-0.8.4.tar.gz': '2e7573632e6454cf6b99d7aac4ccca54be06da05aca2ef7423d22d27d4d4bcd8'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'},
+    {'ppv-lite86-0.2.10.tar.gz': 'ac74c624d6b2d21f425f752262f42188365d7b8ff1aff74c82e45136510a4857'},
+    {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'},
+    {'getrandom-0.2.3.tar.gz': '7fcd999463524c52659517fe2cea98493cfe485d10565e7b0fb07dbba7ad2753'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'},
+    {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'},
+    {'remove_dir_all-0.5.3.tar.gz': '3acd125665422973a33ac9d3dd2df85edad0f4ae9b00dafb1a05e43a9f5ef8e7'},
+    {'redox_syscall-0.2.10.tar.gz': '8383f39639269cde97d255a32bdb68c047337295414940c68bdd30c2e13203ff'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'},
+    {'curl-sys-0.4.49+curl-7.79.1.tar.gz': 'e0f44960aea24a786a46907b8824ebc0e66ca06bf4e4978408c7499620343483'},
+    {'openssl-sys-0.9.67.tar.gz': '69df2d8dfc6ce3aaf44b40dec6f487d5a886516cf6879c49e98e0710f310a058'},
+    {'rand_hc-0.3.1.tar.gz': 'd51e9f596de227fda2ea6c84607f5558e196eeaf43c986b724ba4fb8fdf497e7'},
+    {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'openssl-src-111.16.0+1.1.1l.tar.gz': '7ab2173f69416cf3ec12debb5823d244127d23a9b127d5a5189aa97c5fa2859f'},
+    {'wasi-0.10.2+wasi-snapshot-preview1.tar.gz': 'fd6fbd9a79829dd1ad0cc20627bf1ed606756a7f77edff7b66b7064f9cb327c6'},
+]
 
 builddependencies = [
     ('binutils', '2.36.1'),

From f2684acbfff6f367aa1b9b7d1d7f89902cd999c4 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 10 May 2023 18:36:30 +0200
Subject: [PATCH 518/601] add missing FastTreeMP binary for FastTree

---
 .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb | 5 +++++
 .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb | 5 +++++
 .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb | 5 +++++
 .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb | 5 +++++
 4 files changed, 20 insertions(+)

diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb
index 11318dc50bb..2d4bc28f2bd 100644
--- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb
@@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -
 
 files_to_copy = [(['FastTree'], 'bin')]
 
+# as FastTree is built with OpenMP, the correct binary is FastTreeMP
+# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility
+# see http://www.microbesonline.org/fasttree/#OpenMP
+postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP']
+
 sanity_check_paths = {
     'files': ['bin/FastTree'],
     'dirs': [],
diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb
index ad1c23f20f5..fdcb06c67f3 100644
--- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb
@@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -
 
 files_to_copy = [(['FastTree'], 'bin')]
 
+# as FastTree is built with OpenMP, the correct binary is FastTreeMP
+# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility
+# see http://www.microbesonline.org/fasttree/#OpenMP
+postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP']
+
 sanity_check_paths = {
     'files': ['bin/FastTree'],
     'dirs': [],
diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb
index 51f3e343ef9..9bbfa3f435b 100644
--- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb
+++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb
@@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -
 
 files_to_copy = [(['FastTree'], 'bin')]
 
+# as FastTree is built with OpenMP, the correct binary is FastTreeMP
+# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility
+# see http://www.microbesonline.org/fasttree/#OpenMP
+postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP']
+
 sanity_check_paths = {
     'files': ['bin/FastTree'],
     'dirs': [],
diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb
index a79c7a054da..c1bb41ac734 100644
--- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb
@@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -
 
 files_to_copy = [(['FastTree'], 'bin')]
 
+# as FastTree is built with OpenMP, the correct binary is FastTreeMP
+# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility
+# see http://www.microbesonline.org/fasttree/#OpenMP
+postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP']
+
 sanity_check_paths = {
     'files': ['bin/FastTree'],
     'dirs': [],

From 3757fc78506ade7f14b39c01851978e0ce104256 Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <viktor.rehnberg@gmail.com>
Date: Thu, 11 May 2023 10:37:53 +0200
Subject: [PATCH 519/601] adding easyconfigs:
 pytesseract-0.3.10-GCCcore-11.3.0.eb and patches:
 pytesseract-0.3.10_relax-packaging-version-requirements.patch

---
 .../pytesseract-0.3.10-GCCcore-11.3.0.eb      | 38 +++++++++++++++++++
 ...relax-packaging-version-requirements.patch | 14 +++++++
 2 files changed, 52 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch

diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..f7fbc2c5f56
--- /dev/null
+++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'PythonPackage'
+
+name = 'pytesseract'
+version = '0.3.10'
+
+homepage = "https://github.com/madmaze/pytesseract"
+description = """Python-tesseract is an optical character recognition (OCR)
+tool for python. That is, it will recognize and "read" the text embedded in
+images.
+
+Python-tesseract is a wrapper for Google's Tesseract-OCR Engine. It is also
+useful as a stand-alone invocation script to tesseract, as it can read all
+image types supported by the Pillow and Leptonica imaging libraries, including
+jpeg, png, gif, bmp, tiff, and others. Additionally, if used as a script,
+Python-tesseract will print the recognized text instead of writing it to a
+file."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['pytesseract-0.3.10_relax-packaging-version-requirements.patch']
+checksums = [{
+    SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f',
+    'pytesseract-0.3.10_relax-packaging-version-requirements.patch': \
+        '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6',
+}]
+
+dependencies = [
+    ('tesseract', '5.3.0'),
+    ('Python', '3.10.4'),
+    ('Pillow', '9.1.1'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch
new file mode 100644
index 00000000000..90471c98279
--- /dev/null
+++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch
@@ -0,0 +1,14 @@
+Packaging is used with Version, parse and InvalidVersion that does not strictly
+need the versions specified in setup.cfg
+Author: Viktor Rehnberg
+--- ./setup.cfg.orig	2023-05-11 10:30:41.231633193 +0200
++++ ./setup.cfg	2023-05-11 10:33:01.127272708 +0200
+@@ -27,7 +27,7 @@
+ packages = find:
+ include_package_data = True
+ install_requires = 
+-	packaging>=21.3
++	packaging>=20.9
+ 	Pillow>=8.0.0
+ python_requires = >=3.7
+ 

From 0e14d223649e44c3270ca261c9a27b0a351a12ed Mon Sep 17 00:00:00 2001
From: Thomas Hayward-Schneider <thomas.hayward@ipp.mpg.de>
Date: Thu, 11 May 2023 10:40:30 +0200
Subject: [PATCH 520/601] Switch ftp to http for texlive repos

---
 .../t/texlive/texlive-20200406-GCCcore-8.3.0.eb           | 8 ++++----
 .../easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb  | 2 +-
 .../easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb  | 2 +-
 .../easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb  | 6 +++---
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb
index 4e8bf18c2f4..27046de748b 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb
@@ -45,11 +45,11 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
-    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
+    ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {
-    'PATH': 'bin/x86_64-linux',
+    'PATH': 'bin/%(arch)s-linux',
     'INFOPATH': 'texmf-dist/doc/info',
     'MANPATH': 'texmf-dist/doc/man',
 }
@@ -58,8 +58,8 @@ modextravars = {
 }
 
 sanity_check_paths = {
-    'files': ['bin/x86_64-linux/tex', 'bin/x86_64-linux/latex'],
-    'dirs': ['bin/x86_64-linux', 'texmf-dist'],
+    'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'],
+    'dirs': ['bin/%(arch)s-linux', 'texmf-dist'],
 }
 
 moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb
index 86aa9943d93..97dde3d44ad 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb
@@ -45,7 +45,7 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
-    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
+    ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {
diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb
index 7f55d4478f9..dc4af0f23ae 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb
@@ -45,7 +45,7 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
-    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
+    ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {
diff --git a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb
index 014f57053c8..46445148922 100644
--- a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb
@@ -15,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y
 toolchain = {'name': 'GCC', 'version': '11.2.0'}
 
 source_urls = [
-    'ftp://tug.org/texlive/historic/2022/',
-    'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2022/',
+    'ftp://tug.org/texlive/historic/%s/' % local_version_year,
+    'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year,
 ]
 sources = [
     {
@@ -45,7 +45,7 @@ postinstallcmds = [
     'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && '
     'echo "TEXMFSYSVAR    %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && '
     '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile'
-    ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year
+    ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year
 ]
 
 modextrapaths = {

From 80eb4272c099061c46f78da4180ce513f8457137 Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <viktor.rehnberg@gmail.com>
Date: Thu, 11 May 2023 10:42:15 +0200
Subject: [PATCH 521/601] Fix style

---
 .../p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb          | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
index f7fbc2c5f56..2dc6d2f4d67 100644
--- a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
@@ -21,7 +21,7 @@ sources = [SOURCELOWER_TAR_GZ]
 patches = ['pytesseract-0.3.10_relax-packaging-version-requirements.patch']
 checksums = [{
     SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f',
-    'pytesseract-0.3.10_relax-packaging-version-requirements.patch': \
+    'pytesseract-0.3.10_relax-packaging-version-requirements.patch':
         '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6',
 }]
 

From 65b4c8c12f1de71f6b3c9303653e6bfcbc607a44 Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <viktor.rehnberg@gmail.com>
Date: Thu, 11 May 2023 11:19:24 +0200
Subject: [PATCH 522/601] Fix checksum list semantics

---
 .../p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
index 2dc6d2f4d67..454b392c46c 100644
--- a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
@@ -19,11 +19,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['pytesseract-0.3.10_relax-packaging-version-requirements.patch']
-checksums = [{
-    SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f',
-    'pytesseract-0.3.10_relax-packaging-version-requirements.patch':
-        '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6',
-}]
+checksums = [
+    {SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f'},
+    {'pytesseract-0.3.10_relax-packaging-version-requirements.patch':
+     '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6'},
+]
 
 dependencies = [
     ('tesseract', '5.3.0'),

From e08cac308df6d0f9709f8fb5c560f7cdfb81725e Mon Sep 17 00:00:00 2001
From: Vital-IT <vitsoft@sib.swiss>
Date: Thu, 11 May 2023 15:13:20 +0200
Subject: [PATCH 523/601] adding easyconfigs: Go-1.20.4.eb

---
 easybuild/easyconfigs/g/Go/Go-1.20.4.eb | 31 +++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/Go/Go-1.20.4.eb

diff --git a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
new file mode 100644
index 00000000000..082ea644519
--- /dev/null
+++ b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
@@ -0,0 +1,31 @@
+# Update to 1.20.4
+# Jordi Camps / CNAG
+# Sebastien Moretti / SIB
+
+easyblock = 'Tarball'
+
+name = 'Go'
+version = "1.20.4"
+
+homepage = 'https://www.golang.org'
+description = """Go is an open source programming language that makes it easy to build
+ simple, reliable, and efficient software."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://storage.googleapis.com/golang/']
+
+local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'}
+sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]]
+checksums = ['698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd']
+
+sanity_check_paths = {
+    'files': ['bin/go', 'bin/gofmt'],
+    'dirs': ['api', 'doc', 'lib', 'pkg'],
+}
+
+sanity_check_commands = ["go help"]
+
+modextravars = {'GOROOT': '%(installdir)s'}
+
+moduleclass = 'compiler'

From 57d83da9b7059eceab16126a2ddb27b138536624 Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <viktor.rehnberg@gmail.com>
Date: Thu, 11 May 2023 15:27:37 +0200
Subject: [PATCH 524/601] Add binutils as builddependency

---
 .../p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb        | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
index 454b392c46c..3f3e9090b61 100644
--- a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb
@@ -25,6 +25,10 @@ checksums = [
      '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6'},
 ]
 
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
 dependencies = [
     ('tesseract', '5.3.0'),
     ('Python', '3.10.4'),

From f178a5ac4ff4270845680f66e614624b06133307 Mon Sep 17 00:00:00 2001
From: Vital-IT <vitsoft@sib.swiss>
Date: Thu, 11 May 2023 16:34:45 +0200
Subject: [PATCH 525/601] Add the checksum for the other arch

---
 easybuild/easyconfigs/g/Go/Go-1.20.4.eb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
index 082ea644519..2291970e9da 100644
--- a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
+++ b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
@@ -17,7 +17,10 @@ source_urls = ['https://storage.googleapis.com/golang/']
 
 local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'}
 sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]]
-checksums = ['698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd']
+checksums = [
+    '698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd',  # amd64
+    '105889992ee4b1d40c7c108555222ca70ae43fccb42e20fbf1eebb822f5e72c6',  # arm64
+]
 
 sanity_check_paths = {
     'files': ['bin/go', 'bin/gofmt'],

From 0b40e04972bbacd929ca56fb2f58396dbbd86bce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 12 May 2023 10:32:08 +0200
Subject: [PATCH 526/601] Fix broken multi arch checksums for Go 1.18.3

---
 easybuild/easyconfigs/g/Go/Go-1.18.3.eb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb
index cb532faf480..fc45e80f1eb 100644
--- a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb
+++ b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb
@@ -16,7 +16,10 @@ source_urls = ['https://storage.googleapis.com/golang/']
 
 local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'}
 sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]]
-checksums = ['956f8507b302ab0bb747613695cdae10af99bbd39a90cae522b7c0302cc27245']
+checksums = [{
+    'go%(version)s.linux-amd64.tar.gz': '956f8507b302ab0bb747613695cdae10af99bbd39a90cae522b7c0302cc27245',
+    'go%(version)s.linux-arm64.tar.gz': 'beacbe1441bee4d7978b900136d1d6a71d150f0a9bb77e9d50c822065623a35a',
+}]
 
 sanity_check_paths = {
     'files': ['bin/go', 'bin/gofmt'],

From 23029fe33fa68e8d1ced9322ecf88edf8c7dbe1e Mon Sep 17 00:00:00 2001
From: Vital-IT <vitsoft@sib.swiss>
Date: Fri, 12 May 2023 11:04:57 +0200
Subject: [PATCH 527/601] Fix broken multi arch checksums

---
 easybuild/easyconfigs/g/Go/Go-1.20.4.eb | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
index 2291970e9da..a294c0de68f 100644
--- a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
+++ b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb
@@ -17,10 +17,10 @@ source_urls = ['https://storage.googleapis.com/golang/']
 
 local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'}
 sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]]
-checksums = [
-    '698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd',  # amd64
-    '105889992ee4b1d40c7c108555222ca70ae43fccb42e20fbf1eebb822f5e72c6',  # arm64
-]
+checksums = [{
+    'go%(version)s.linux-amd64.tar.gz': '698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd',
+    'go%(version)s.linux-arm64.tar.gz': '105889992ee4b1d40c7c108555222ca70ae43fccb42e20fbf1eebb822f5e72c6',
+}]
 
 sanity_check_paths = {
     'files': ['bin/go', 'bin/gofmt'],

From 7f62900e873efd9a1c30e6dab59077fcad9a947b Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Mon, 15 May 2023 16:23:00 +0200
Subject: [PATCH 528/601] using cpc2 made for python3

---
 .../c/CPC2/CPC2-1.0.1-foss-2022a.eb           | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
new file mode 100644
index 00000000000..f03104d04f7
--- /dev/null
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
@@ -0,0 +1,39 @@
+easyblock = 'PackedBinary'
+
+name = 'CPC2'
+version = '1.0.1'
+
+homepage = 'http://cpc2.cbi.pku.edu.cn'
+description = """ a fast and accurate coding potential calculator based on sequence intrinsic features  """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available
+# download from github mirror
+source_urls = ['https://github.com/gao-lab/CPC2_standalone/archive/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
+checksums = ['31f3d1e2466aea25f03ffcb5abd4556cd17862ef65ed3a1e42f3d99665529d08']
+
+local_svm_orig = "lib_dir + \"libsvm/libsvm-3.18/"
+
+postinstallcmds = [
+    "sed -i 's|" + local_svm_orig + "svm-scale\"|\"$EBROOTLIBSVM/bin/svm-scale\"|g' %(installdir)s/bin/CPC2.py",
+    "sed -i 's|" + local_svm_orig + "svm-predict\"|\"$EBROOTLIBSVM/bin/svm-predict\"|g' %(installdir)s/bin/CPC2.py",
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('LIBSVM', '3.30'),
+    ('Biopython', '1.79'),
+]
+
+install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/'
+
+sanity_check_paths = {
+    'files': ['bin/CPC2.py'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out']
+
+moduleclass = 'lib'

From 8a93adc8b8693cebc5af0d48df582e5fb9ce3831 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Mon, 15 May 2023 16:25:01 +0200
Subject: [PATCH 529/601] Delete CPC2-0.1_fix_libsvm_path_and_python2.patch

unnecessary, as source files for python3 were found
---
 ...CPC2-0.1_fix_libsvm_path_and_python2.patch | 82 -------------------
 1 file changed, 82 deletions(-)
 delete mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch b/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch
deleted file mode 100644
index 38190f1c201..00000000000
--- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-Use libsvm from the environment instead of the one provided with CPC2
-Author: Samuel Moors, Vrije Universiteit Brussel (VUB)
-Update: Fix incompatible syntax with Python 3
-Updated by: Denis Kristak (Inuits)
-diff -ruN cpc2_orig/bin/compress.py cpc2/bin/compress.py
---- cpc2_orig/bin/compress.py	2018-10-22 17:58:22.000000000 +0200
-+++ cpc2/bin/compress.py	2023-05-03 12:37:36.240001307 +0200
-@@ -11,7 +11,7 @@
- 			fq_fp = gzip.open(fq_file,mode+"b",level)
- 		else:
- 			sys.stderr.write("[INFO] read file '%s'\n"%fq_file)
--			fq_fp = file(fq_file,mode)
-+			fq_fp = open(fq_file,mode)
- 	except:
- 		sys.stderr.write("Error: Fail to IO file: %s\n"%(fq_file))
- 		sys.exit(1)
-diff -ruN cpc2_orig/bin/CPC2.py cpc2/bin/CPC2.py
---- cpc2_orig/bin/CPC2.py	2023-05-02 16:41:34.222887000 +0200
-+++ cpc2/bin/CPC2.py	2023-05-03 12:40:15.817915000 +0200
-@@ -78,7 +78,7 @@
- 		'''
- 		while True:
- 			try: 
--				codon,index = triplet_got.next()
-+				codon,index = next(triplet_got)
- 			except StopIteration:
- 				break 
- 			if codon in starts and codon not in stops:
-@@ -89,7 +89,7 @@
- 				end_extension = False
- 				while True:
- 					try: 
--						codon,index = triplet_got.next()
-+						codon,index = next(triplet_got)
- 					except StopIteration:
- 						end_extension = True
- 						integrity = -1
-@@ -245,9 +245,9 @@
- 	'''
- 	strinfoAmbiguous = re.compile("X|B|Z|J|U",re.I)
- 	ptU = re.compile("U",re.I)
--	ftmp_feat = file(outfile + ".feat","w")
--	ftmp_svm = file(outfile + ".tmp.1","w")
--	ftmp_result = file(outfile,"w")
-+	ftmp_feat = open(outfile + ".feat","w")
-+	ftmp_svm = open(outfile + ".tmp.1","w")
-+	ftmp_result = open(outfile,"w")
- 	ftmp_result.write("\t".join(map(str,["#ID","transcript_length","peptide_length","Fickett_score","pI","ORF_integrity","coding_probability","label"]))+"\n")
- 	ftmp_result.close()
- 	fickett_obj = Fickett()
-@@ -288,16 +288,16 @@
- 	script_dir,filename = os.path.split(os.path.abspath(sys.argv[0]))
- 	data_dir = script_dir + "/../data/"
- 	lib_dir = script_dir + "/../libs/"
--	app_svm_scale = lib_dir + "libsvm/libsvm-3.18/svm-scale"
--	app_svm_predict = lib_dir + "libsvm/libsvm-3.18/svm-predict"
--	os.system('test -x '+ app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr')
--	os.system('test -x '+ app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr')
-+	app_svm_scale = 'svm-scale'
-+	app_svm_predict = 'svm-predict'
-+	os.system('which ' + app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr')
-+	os.system('which ' + app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr')
- 	
- 	cmd = app_svm_scale + ' -r ' + data_dir + 'cpc2.range ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&'
- 	cmd = cmd + app_svm_predict + ' -b 1 -q ' + outfile + '.tmp.2 ' + data_dir + 'cpc2.model ' + outfile + '.tmp.1 &&'
- 	cmd = cmd + 'awk -vOFS="\\t" \'{if ($1 == 1){print $2,"coding"} else if ($1 == 0){print $2,"noncoding"}}\' ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&'
- 	cmd = cmd + 'paste ' + outfile + '.feat ' + outfile + '.tmp.2 >>' + outfile
--	command = suprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-+	command = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- 	(outtext, errtext) = command.communicate()
- 	exitstatus = command.returncode
- 	os.system('rm -f ' + outfile + '.tmp.1 ' + outfile + '.tmp.2')
-@@ -306,7 +306,8 @@
- 	#	pass
- 	if exitstatus == 0:
- 		rm_cmd = "rm -f " + outfile + '.feat'
--		subprocess.call(rm_cmd)
-+		print(rm_cmd)
-+		subprocess.run(rm_cmd, shell=True)
- 		sys.stderr.write("[INFO] Running Done!\n")
- 		return 0
- 	else:

From 9b71436e2705f060e827578a2aca0c92486bc534 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Mon, 15 May 2023 16:25:37 +0200
Subject: [PATCH 530/601] Delete CPC2-0.1-foss-2022a.eb

removing, as src files for py3 were found (and version change was necessary, renaming the file)
---
 .../easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 40 -------------------
 1 file changed, 40 deletions(-)
 delete mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
deleted file mode 100644
index e2ffcd2d854..00000000000
--- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb
+++ /dev/null
@@ -1,40 +0,0 @@
-# Author: Samuel Moors, Vrije Universiteit Brussel (VUB)
-# Updated: Denis Kristak (Inuits)
-# Update to a Python3 version
-easyblock = 'PackedBinary'
-
-name = 'CPC2'
-version = '0.1'
-local_commit = '813487e'
-
-homepage = 'http://cpc2.gao-lab.org/'
-description = """ a fast and accurate coding potential calculator based on sequence intrinsic features  """
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available
-# download from github mirror
-source_urls = ['https://github.com/lucventurini/CPC2/archive/']
-sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
-patches = ['%(name)s-%(version)s_fix_libsvm_path_and_python2.patch']
-checksums = [
-    {'CPC2-0.1.tar.gz': '6fd4f3fb05b179073709c033481ae082085eabc7c5281cd743c9419d3ec6de67'},
-    {'CPC2-0.1_fix_libsvm_path_and_python2.patch': '657f552ebfad925e8c051a19426cd5bb1b8ad7da8cdcc3e701e1220673330842'},
-]
-
-dependencies = [
-    ('Python', '3.10.4'),
-    ('LIBSVM', '3.30'),
-    ('Biopython', '1.79'),
-]
-
-install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/'
-
-sanity_check_paths = {
-    'files': ['bin/CPC2.py'],
-    'dirs': ['data'],
-}
-
-sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out']
-
-moduleclass = 'lib'

From 7f48b5ecd0c076ff6e01a45d507292910ea8d53d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 15 May 2023 17:41:38 +0200
Subject: [PATCH 531/601] adding easyconfigs: vsc-mympirun-5.3.1.eb

---
 .../v/vsc-mympirun/vsc-mympirun-5.3.1.eb      | 64 +++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb

diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb
new file mode 100644
index 00000000000..944357dedd6
--- /dev/null
+++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb
@@ -0,0 +1,64 @@
+easyblock = 'PythonBundle'
+
+name = 'vsc-mympirun'
+version = '5.3.1'
+
+homepage = 'https://github.com/hpcugent/vsc-mympirun'
+description = """mympirun is a tool to make it easier for users of HPC clusters to
+run MPI programs with good performance."""
+
+# we build this to work with every python version
+toolchain = SYSTEM
+
+allow_system_deps = [('Python', SYS_PYTHON_VERSION)]
+
+use_pip = False
+
+exts_list = [
+    ('setuptools', '41.6.0', {
+        'source_tmpl': '%(name)s-%(version)s.zip',
+        'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'],
+    }),
+    ('future', '0.18.3', {
+        'checksums': ['34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307'],
+    }),
+    ('pbr', '5.11.1', {
+        'checksums': ['aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3'],
+    }),
+    ('funcsigs', '1.0.2', {
+        'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'],
+    }),
+    ('mock', '5.0.2', {
+        'checksums': ['06f18d7d65b44428202b145a9a36e99c2ee00d1eb992df0caf881d4664377891'],
+    }),
+    ('IPy', '1.01', {
+        'modulename': 'IPy',
+        'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'],
+    }),
+    ('vsc-install', '0.18.5', {
+        'modulename': 'vsc.install',
+        'checksums': ['90e00ddde9d394fdb5426f6f4d466425c69acded3fdf25ce73a0b345f6afc036'],
+    }),
+    ('vsc-base', '3.5.3', {
+        'modulename': 'vsc.utils',
+        'checksums': ['7c4df43fc0508d6857acf8127deb1088b899cd364a14c688dac2d61617579ba9'],
+    }),
+    (name, version, {
+        'modulename': False,
+        'checksums': ['67fb89855044678e595fef39415aafdd26a1a9a4c89b3f89a4d34a1824df7bcf'],
+    }),
+]
+
+# we ship something in bin/fake
+modextrapaths = {'PATH': 'bin/fake'}
+
+sanity_check_paths = {
+    'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'],
+    'dirs': ['bin/fake'],
+}
+sanity_check_commands = ["mympirun --help"]
+
+# can't enable 'pip check' since pip may not be installed in OS
+sanity_pip_check = False
+
+moduleclass = 'tools'

From ae4f9c64fd60825b43976258007742b8dd2a58af Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Mon, 15 May 2023 20:10:22 +0200
Subject: [PATCH 532/601] Annocript + small change to BioPerl

---
 .../Annocript-2.0-foss-2022a-Python-3.10.4.eb | 77 +++++++++++++++++++
 .../a/Annocript/annocript_fix_paths.patch     | 36 +++++++++
 .../a/Annocript/annocript_no_background.patch | 23 ++++++
 .../b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb |  7 +-
 4 files changed, 142 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
 create mode 100644 easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch
 create mode 100644 easybuild/easyconfigs/a/Annocript/annocript_no_background.patch

diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
new file mode 100644
index 00000000000..4c30feb8389
--- /dev/null
+++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
@@ -0,0 +1,77 @@
+easyblock = 'PackedBinary'
+
+name = 'Annocript'
+version = '2.0'
+local_commit = '84fd67b'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://github.com/frankMusacchia/Annocript'
+description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes.
+ It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division
+ adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways.
+ Annocript also gives information about the longest ORF and the non-coding potential using external software.
+ Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology
+ and sequence features. """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/frankMusacchia/Annocript/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+patches = [
+    'annocript_fix_paths.patch',
+    'annocript_no_background.patch',
+]
+checksums = [
+    {'Annocript-2.0.tar.gz': '151dec3a390826fd2bcc7d794a9565535702dfc9c4672842e825a9fcf21406d9'},
+    {'annocript_fix_paths.patch': '95359e335a6a992f5f269e8f199c9df92d765f7ff41890298acead12d562685c'},
+    {'annocript_no_background.patch': 'ca02c2b02b7574c25128c9a4ce2b69a13a0bb2b409efd2ea63562053bf2e2c57'},
+]
+
+dependencies = [
+    ('Compress-Raw-Zlib', '2.202'),
+    ('Python', '3.10.4'),
+    ('Perl', '5.34.1'),
+    ('BioPerl', '1.7.8'),
+    ('R', '4.2.1'),
+    ('CPC2', '1.0.1'),
+    ('BLAST+', '2.13.0'),
+    ('LIBSVM', '3.30'),
+    ('MariaDB', '10.9.3'),
+    ('DBD-mysql', '4.050'),
+]
+
+postinstallcmds = [
+    # Extract dna2pep to annocript's bin folder, set permissions.
+    # It is just a series Python scripts and I'm not building it as a standalone dependency, as sources for this SW
+    # are not available elsewhere than in the Annocript repository anyway.
+    "mkdir %(installdir)s/bin ",
+    "cp %(builddir)s/Annocript-*/DL_PROGRAMS/dna2pep-1.1.tar.gz %(installdir)s/bin ",
+    "cd %(installdir)s/bin && tar -zxvf dna2pep-1.1.tar.gz ",
+    "rm %(installdir)s/bin/dna2pep-1.1.tar.gz && chmod 755 %(installdir)s/bin/dna2pep-1.1/dna2pep.py ",
+    # extract annocript itself
+    'mv %(installdir)s/annocript.pl %(installdir)s/bin/',
+    'sed -i -e "1s|#!.*$|#!/usr/bin/env perl|g" %(installdir)s/bin/annocript.pl',
+    'chmod a+rx %(installdir)s/bin/annocript.pl',
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('CGI', '4.43', {
+        'source_tmpl': 'CGI-4.43.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'],
+        'checksums': ['14b94f9df6e48fc26ebc4fa1e01a7b534cbc1611028a49028f9ac9d8ca27b734'],
+    }),
+]
+
+modextrapaths = {'PERL5LIB': ['', 'lib/perl5/site_perl/%(perlver)s/']}
+
+sanity_check_paths = {
+    'files': ['bin/annocript.pl'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['annocript.pl --help']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch b/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch
new file mode 100644
index 00000000000..c863a8425a1
--- /dev/null
+++ b/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch
@@ -0,0 +1,36 @@
+Do not use full paths for executables in the config file: they should be in the PATH
+Author: Samuel Moors, Vrije Universiteit Brussel (VUB)
+diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/CONFIGURATION/config_user.txt Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/CONFIGURATION/config_user.txt
+--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/CONFIGURATION/config_user.txt	2023-05-15 18:02:35.946010508 +0200
++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/CONFIGURATION/config_user.txt	2023-05-15 18:04:08.262818993 +0200
+@@ -114,7 +114,7 @@
+ 
+ #Programs Paths
+ diamondPath =
+-blastPath = /home/francesco/bin/ncbi-blast-2.7.1+/bin/
+-lncRNAPredProgPath = /home/francesco/bin/CPC2-beta/bin/CPC2.py
+-dna2pepPath = /home/francesco/bin/dna2pep-1.1/dna2pep.py
++blastPath =
++lncRNAPredProgPath = CPC2.py
++dna2pepPath = dna2pep.py
+ ##############################
+diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/LIB/annocript_management.pm Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/LIB/annocript_management.pm
+--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/LIB/annocript_management.pm	2023-05-15 18:02:36.477018945 +0200
++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/LIB/annocript_management.pm	2023-05-15 18:05:42.646383000 +0200
+@@ -748,9 +748,15 @@
+ 
+   #Here we collect the path to the programs using an array initialized in the beginning of the page
+   # with all the programs used by Annocript
++  # first expand executables to full path
++  use File::Which;
+   foreach my $program (@$blastProgramsInUse){
+     my $var= $program.'Path';
+-    $configHash->{$var} = $configHash->{'blastPath'}.$program;
++    $configHash->{$var} = which($program) or die "error: blast executable $program not found\n";
++  }
++  foreach my $mypath ('lncRNAPredProgPath', 'dna2pepPath', 'makeblastdbPath'){
++    my $myexec = $configHash->{$mypath};
++    $configHash->{$mypath} = which($myexec) or die "error: executable $myexec not found\n";
+   }
+   
+ 	    #CONTROLS THE PATH TO THE PROGRAMS
diff --git a/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch b/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch
new file mode 100644
index 00000000000..cf3b8ef36e3
--- /dev/null
+++ b/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch
@@ -0,0 +1,23 @@
+Do not start perl script in background
+Author: Samuel Moors, Vrije Universiteit Brussel (VUB)
+diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/annocript.pl Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/annocript.pl
+--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/annocript.pl	2023-05-15 18:02:36.827824452 +0200
++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/annocript.pl	2023-05-15 18:13:45.525029000 +0200
+@@ -301,7 +301,7 @@
+ 		  ."\n\nPlease let us know if any problem occurs during the computation or you don't get from Annocript the expected result.\n"
+ 		  ."You may want to use the forum at: https://groups.google.com/forum/#!forum/annocript.\n",$log_file);#DEBUGCODE	
+ 
+-	nice_printing("STARTING ANNOCRIPT IN BACKGROUND! BYE!",$log_file);
++	nice_printing("STARTING ANNOCRIPT IN FOREGROUND! BYE!",$log_file);
+ 
+ 	close ( $logFHandle );
+ 
+@@ -325,7 +325,7 @@
+ 	chdir $program_folder;
+ 	
+ 	#This perl script will be run in background
+-	my $runAnnocriptCmd = "nohup perl ".$configHash->{'ProgExecFolder'} ."/annocript_executor.pl $user_config $program_config $timesFile $configHashPath >> $log_file &";
++	my $runAnnocriptCmd = "perl ".$configHash->{'ProgExecFolder'} ."/annocript_executor.pl $user_config $program_config $timesFile $configHashPath >> $log_file";
+ 	( system($runAnnocriptCmd) ) == 0 
+ 	  or die("Unable to start annocript_executor!\n");
+ 	}
diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb
index 5b7057ffa26..72311a255bb 100644
--- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb
@@ -36,7 +36,12 @@ exts_list = [
         'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
         'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'],
     }),
-    ('BioPerl', version, {
+    ('Bio::DB::SeqFeature', '1.7.4', {
+        'source_tmpl': 'Bio-DB-SeqFeature-%(version)s.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
+        'checksums': ['f2304f95fb77a12732b1883817525609e54fa70b2638ed2de0696d503407fe91'],
+    }),
+    (name, version, {
         'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'],
         'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'],
     }),

From 848e40a4447ad3dcccb4a5be364572e79c5c1b2a Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Mon, 15 May 2023 20:14:55 +0200
Subject: [PATCH 533/601] updated moduleclass

---
 .../a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
index 4c30feb8389..aa1f8921915 100644
--- a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
+++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
@@ -74,4 +74,4 @@ sanity_check_paths = {
 
 sanity_check_commands = ['annocript.pl --help']
 
-moduleclass = 'lib'
+moduleclass = 'bio'

From c3a6165d8998d5970807ea7ca0f8502d2771ac8e Mon Sep 17 00:00:00 2001
From: p251204 <p251204@node1>
Date: Tue, 16 May 2023 09:50:12 +0200
Subject: [PATCH 534/601] adding easyconfigs: breseq-0.38.1-foss-2022a.eb

---
 .../b/breseq/breseq-0.38.1-foss-2022a.eb      | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb

diff --git a/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb b/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb
new file mode 100644
index 00000000000..7d1f5285c68
--- /dev/null
+++ b/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'breseq'
+version = '0.38.1'
+
+homepage = 'https://barricklab.org/breseq'
+description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/barricklab/breseq/releases/download/v%(version)s/']
+sources = ['breseq-%(version)s-Source.tar.gz']
+checksums = ['92af34f7248f7c8cf65951e1b86ffc0d6f7446dbe9d3323aa43c577ea1ff48b3']
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('Bowtie2', '2.4.5'),
+    ('zlib', '1.2.12'),
+    ('ncurses', '6.3'),
+]
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/breseq', 'bin/gdtools'],
+    'dirs': [],
+}
+
+# breseq --help exists with non-zero exit code, so use grep
+sanity_check_commands = ["breseq --help | grep 'Usage: breseq'"]
+
+moduleclass = 'bio'

From 9e87e7a00b605d3e16de58e2bf40c256bfc3dc5e Mon Sep 17 00:00:00 2001
From: p251204 <p251204@node1>
Date: Tue, 16 May 2023 10:31:43 +0200
Subject: [PATCH 535/601] adding easyconfigs: PALEOMIX-1.3.7-foss-2022a.eb,
 seqtk-1.3-GCC-11.3.0.eb, mapDamage-2.2.1-foss-2022a.eb

---
 .../m/mapDamage/mapDamage-2.2.1-foss-2022a.eb | 36 ++++++++++++++
 .../p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb   | 48 +++++++++++++++++++
 .../s/seqtk/seqtk-1.3-GCC-11.3.0.eb           | 33 +++++++++++++
 3 files changed, 117 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb
new file mode 100644
index 00000000000..500f6c287a4
--- /dev/null
+++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonPackage'
+
+name = 'mapDamage'
+version = '2.2.1'
+
+github_account = 'ginolhac'
+
+homepage = 'https://ginolhac.github.io/mapDamage/'
+description = """mapDamage2 is a computational framework written in Python and
+    R, which tracks and quantifies DNA damage patterns among ancient DNA
+    sequencing reads generated by Next-Generation Sequencing platforms."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+patches = ['%(name)s-2.2.1_use-external-seqtk.patch']
+checksums = [
+    'f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c',  # 2.2.1.tar.gz
+    'f01a90c29123460f8cb6ba2fe0f42e9ec66b0febff430d4ec4f0ab1197c552e7',  # mapDamage-2.2.1_use-external-seqtk.patch
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('seqtk', '1.3'),
+    ('Pysam', '0.19.1'),
+    ('R', '4.2.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = True
+
+sanity_check_commands = ['mapDamage --help']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
new file mode 100644
index 00000000000..c9b7f7186e6
--- /dev/null
+++ b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'PALEOMIX'
+version = '1.3.7'
+
+homepage = 'https://github.com/MikkelSchubert/paleomix'
+description = """The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing
+ of High-Throughput Sequencing (HTS) data."""
+
+toolchain = {'name' : 'foss', 'version' : '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SAMtools', '1.16.1'),
+    ('AdapterRemoval', '2.3.3'),
+    ('picard', '3.0.0', '-Java-17', SYSTEM),
+    ('Bowtie2', '2.4.5'),
+    ('mapDamage', '2.2.1'),
+    ('Pysam', '0.19.1'),
+    ('ruamel.yaml', '0.17.21'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('humanfriendly', '10.0', {
+        'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'],
+    }),
+    ('coloredlogs', '15.0.1', {
+        'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'],
+    }),
+    ('ConfigArgParse', '1.5.3', {
+        'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'],
+    }),
+    ('setproctitle', '1.3.2', {
+        'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'],
+    }),
+    (name, version, {
+        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
+        'checksums': ['effc402cd4207916ee062edf68b18b21b6c1adc596eea30d58805a75c8652767'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ['paleomix --help']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb
new file mode 100644
index 00000000000..165375a4e10
--- /dev/null
+++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb
@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'seqtk'
+version = '1.3'
+
+homepage = 'https://github.com/lh3/seqtk/'
+description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
+ It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'lh3'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563']
+
+dependencies = [('zlib', '1.2.12')]
+
+skipsteps = ['configure']
+
+buildopts = 'CC="$CC" CFLAGS="$CLFAGS"'
+
+preinstallopts = "mkdir %(installdir)s/bin && "
+installopts = 'BINDIR=%(installdir)s/bin/'
+
+sanity_check_paths = {
+    'files': ['bin/seqtk'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["seqtk 2>&1 | grep 'Usage:[ ]*seqtk'"]
+
+moduleclass = 'bio'

From 950678994ec0c5d5819d148bb2f8f53a217ade08 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 May 2023 10:54:51 +0200
Subject: [PATCH 536/601] use picard 2.25.1

---
 easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
index c9b7f7186e6..e2b4d2246f8 100644
--- a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
@@ -13,7 +13,7 @@ dependencies = [
     ('Python', '3.10.4'),
     ('SAMtools', '1.16.1'),
     ('AdapterRemoval', '2.3.3'),
-    ('picard', '3.0.0', '-Java-17', SYSTEM),
+    ('picard', '2.25.1', '-Java-11', SYSTEM),
     ('Bowtie2', '2.4.5'),
     ('mapDamage', '2.2.1'),
     ('Pysam', '0.19.1'),

From f8c4e498e408d4bf3053bc2d3e7f8874ea16aa80 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 May 2023 11:17:13 +0200
Subject: [PATCH 537/601] remove whitespaces

---
 easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
index e2b4d2246f8..b145680d1ec 100644
--- a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb
@@ -7,7 +7,7 @@ homepage = 'https://github.com/MikkelSchubert/paleomix'
 description = """The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing
  of High-Throughput Sequencing (HTS) data."""
 
-toolchain = {'name' : 'foss', 'version' : '2022a'}
+toolchain = {'name': 'foss', 'version': '2022a'}
 
 dependencies = [
     ('Python', '3.10.4'),

From ff933f3dce0eb97275459f6cbe433f4159b3f840 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 16 May 2023 11:55:40 +0200
Subject: [PATCH 538/601] adding easyconfigs:
 Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb,
 Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb

---
 ...7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb | 37 +++++++++++++++++++
 ...aindecode-0.7-foss-2021a-PyTorch-1.10.2.eb | 36 ++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb
 create mode 100644 easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb

diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb
new file mode 100644
index 00000000000..6e6c6ca13e1
--- /dev/null
+++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb
@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'Braindecode'
+version = '0.7'
+versionsuffix = '-PyTorch-1.10.2-CUDA-%(cudaver)s'
+
+homepage = 'https://braindecode.org/'
+description = """Braindecode is an open-source Python toolbox for decoding raw
+electrophysiological brain data with deep learning models. It includes dataset
+fetchers, data preprocessing and visualization tools, as well as
+implementations of several deep learning architectures and data augmentations
+for analysis of EEG, ECoG and MEG."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+dependencies = [
+    ('CUDA', '11.3.1', '', SYSTEM),
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('h5py', '3.2.1'),
+    ('matplotlib', '3.4.2'),
+    ('MNE-Python', '0.24.1'),
+    ('MOABB', '0.4.6'),
+    ('skorch', '0.11.0', versionsuffix),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['e2bca3d096b70b041d7b30ca2dfeaffae79ea722a4578cee04c9864ec07effce'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb
new file mode 100644
index 00000000000..c503d33df9c
--- /dev/null
+++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb
@@ -0,0 +1,36 @@
+easyblock = 'PythonBundle'
+
+name = 'Braindecode'
+version = '0.7'
+versionsuffix = '-PyTorch-1.10.2'
+
+homepage = 'https://braindecode.org/'
+description = """Braindecode is an open-source Python toolbox for decoding raw
+electrophysiological brain data with deep learning models. It includes dataset
+fetchers, data preprocessing and visualization tools, as well as
+implementations of several deep learning architectures and data augmentations
+for analysis of EEG, ECoG and MEG."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('h5py', '3.2.1'),
+    ('matplotlib', '3.4.2'),
+    ('MNE-Python', '0.24.1'),
+    ('MOABB', '0.4.6'),
+    ('skorch', '0.11.0', versionsuffix),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'checksums': ['e2bca3d096b70b041d7b30ca2dfeaffae79ea722a4578cee04c9864ec07effce'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'ai'

From a41289da5b0bc16fafe031f8d149598c9645464f Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 16 May 2023 12:14:41 +0200
Subject: [PATCH 539/601] adding easyconfigs: CREST-2.11.2-intel-2021a.eb

---
 .../c/CREST/CREST-2.11.2-intel-2021a.eb       | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb

diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb
new file mode 100644
index 00000000000..4746716d31d
--- /dev/null
+++ b/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb
@@ -0,0 +1,32 @@
+# Author: Jasper Grimm (UoY)
+
+easyblock = 'CMakeMake'
+
+name = 'CREST'
+version = '2.11.2'
+
+homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html'
+description = """CREST is an utility/driver program for the xtb program. Originally it was designed
+ as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool,
+ but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally
+ the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb
+ program) and tool for the creation and analysation of structure ensembles.
+"""
+
+toolchain = {'name': 'intel', 'version': '2021a'}
+
+github_account = 'grimme-lab'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['f17da872064eb64502ac24c19e431467940d98dcb1bd391f7267f412a0a79dab']
+
+builddependencies = [('CMake', '3.20.1')]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % name.lower()],
+    'dirs': [],
+}
+
+sanity_check_commands = ["crest -h", "crest --cite"]
+
+moduleclass = 'chem'

From ff15d5374978cd446b9d8b299b140ac257ecc810 Mon Sep 17 00:00:00 2001
From: deniskristak <denis.kristak@gmail.com>
Date: Tue, 16 May 2023 12:15:52 +0200
Subject: [PATCH 540/601] removed python version suffix

---
 .../a/Annocript/Annocript-2.0-foss-2022a.eb   | 76 +++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb

diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb
new file mode 100644
index 00000000000..7efa2268907
--- /dev/null
+++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb
@@ -0,0 +1,76 @@
+easyblock = 'PackedBinary'
+
+name = 'Annocript'
+version = '2.0'
+local_commit = '84fd67b'
+
+homepage = 'https://github.com/frankMusacchia/Annocript'
+description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes.
+ It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division
+ adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways.
+ Annocript also gives information about the longest ORF and the non-coding potential using external software.
+ Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology
+ and sequence features. """
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/frankMusacchia/Annocript/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+patches = [
+    'annocript_fix_paths.patch',
+    'annocript_no_background.patch',
+]
+checksums = [
+    {'Annocript-2.0.tar.gz': '151dec3a390826fd2bcc7d794a9565535702dfc9c4672842e825a9fcf21406d9'},
+    {'annocript_fix_paths.patch': '95359e335a6a992f5f269e8f199c9df92d765f7ff41890298acead12d562685c'},
+    {'annocript_no_background.patch': 'ca02c2b02b7574c25128c9a4ce2b69a13a0bb2b409efd2ea63562053bf2e2c57'},
+]
+
+dependencies = [
+    ('Compress-Raw-Zlib', '2.202'),
+    ('Python', '3.10.4'),
+    ('Perl', '5.34.1'),
+    ('BioPerl', '1.7.8'),
+    ('R', '4.2.1'),
+    ('CPC2', '1.0.1'),
+    ('BLAST+', '2.13.0'),
+    ('LIBSVM', '3.30'),
+    ('MariaDB', '10.9.3'),
+    ('DBD-mysql', '4.050'),
+]
+
+postinstallcmds = [
+    # Extract dna2pep to annocript's bin folder, set permissions.
+    # It is just a series Python scripts and I'm not building it as a standalone dependency, as sources for this SW
+    # are not available elsewhere than in the Annocript repository anyway.
+    "mkdir %(installdir)s/bin ",
+    "cp %(builddir)s/Annocript-*/DL_PROGRAMS/dna2pep-1.1.tar.gz %(installdir)s/bin ",
+    "cd %(installdir)s/bin && tar -zxvf dna2pep-1.1.tar.gz ",
+    "rm %(installdir)s/bin/dna2pep-1.1.tar.gz && chmod 755 %(installdir)s/bin/dna2pep-1.1/dna2pep.py ",
+    # extract annocript itself
+    'mv %(installdir)s/annocript.pl %(installdir)s/bin/',
+    'sed -i -e "1s|#!.*$|#!/usr/bin/env perl|g" %(installdir)s/bin/annocript.pl',
+    'chmod a+rx %(installdir)s/bin/annocript.pl',
+]
+
+exts_defaultclass = 'PerlModule'
+exts_filter = ("perldoc -lm %(ext_name)s ", "")
+
+exts_list = [
+    ('CGI', '4.43', {
+        'source_tmpl': 'CGI-4.43.tar.gz',
+        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'],
+        'checksums': ['14b94f9df6e48fc26ebc4fa1e01a7b534cbc1611028a49028f9ac9d8ca27b734'],
+    }),
+]
+
+modextrapaths = {'PERL5LIB': ['', 'lib/perl5/site_perl/%(perlver)s/']}
+
+sanity_check_paths = {
+    'files': ['bin/annocript.pl'],
+    'dirs': [],
+}
+
+sanity_check_commands = ['annocript.pl --help']
+
+moduleclass = 'bio'

From d455e4779699305d261f54c6a5bb2b446291eac5 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Tue, 16 May 2023 12:16:39 +0200
Subject: [PATCH 541/601] Update
 easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
index f03104d04f7..27e523b16f2 100644
--- a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
@@ -8,8 +8,6 @@ description = """ a fast and accurate coding potential calculator based on seque
 
 toolchain = {'name': 'foss', 'version': '2022a'}
 
-# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available
-# download from github mirror
 source_urls = ['https://github.com/gao-lab/CPC2_standalone/archive/']
 sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}]
 checksums = ['31f3d1e2466aea25f03ffcb5abd4556cd17862ef65ed3a1e42f3d99665529d08']

From 7d1ab2487f5957a877701a135087c9e2105e3396 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Tue, 16 May 2023 12:16:57 +0200
Subject: [PATCH 542/601] Update
 easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Mikael Öhman <micketeer@gmail.com>
---
 easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
index 27e523b16f2..008b9e1c179 100644
--- a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb
@@ -3,7 +3,7 @@ easyblock = 'PackedBinary'
 name = 'CPC2'
 version = '1.0.1'
 
-homepage = 'http://cpc2.cbi.pku.edu.cn'
+homepage = 'http://cpc2.gao-lab.org/'
 description = """ a fast and accurate coding potential calculator based on sequence intrinsic features  """
 
 toolchain = {'name': 'foss', 'version': '2022a'}

From b3d89091a65d21961fe37910d718e475cadec68f Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Tue, 16 May 2023 14:38:54 +0200
Subject: [PATCH 543/601] adding easyconfigs:
 turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb

---
 ...inesFoam-20220516-foss-2020a-OpenFOAM-8.eb | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb

diff --git a/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb
new file mode 100644
index 00000000000..890702f6e8a
--- /dev/null
+++ b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb
@@ -0,0 +1,35 @@
+easyblock = 'CmdCp'
+
+name = 'turbinesFoam'
+version = '20220516'
+_openfoamver = '8'
+_commit = '480eeef'
+versionsuffix = '-OpenFOAM-%s' % _openfoamver
+
+homepage = 'https://github.com/turbinesFoam/turbinesFoam'
+description = """
+turbinesFoam is a library for simulating wind and marine hydrokinetic turbines
+in OpenFOAM using the actuator line method.
+"""
+
+toolchain = {'name': 'foss', 'version': '2020a'}
+
+github_account = 'turbinesFoam'
+source_urls = [GITHUB_SOURCE]
+sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['2e13faec8b2489e91108ea3fc8eb31b1b32bb1478e608853c9cfa9b78a3206d1']
+
+dependencies = [
+    ('OpenFOAM', _openfoamver),
+]
+
+cmds_map = [('.*', 'source "$FOAM_BASH" && FOAM_USER_LIBBIN="$PWD/lib" ./Allwmake')]
+
+files_to_copy = ['lib']
+
+sanity_check_paths = {
+    'files': ['lib/libturbinesFoam.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

From 69ba59461cad53ae229742f69cf0ab3502273d4b Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <Balazs.Hajgato@UGent.be>
Date: Tue, 16 May 2023 21:05:02 +0200
Subject: [PATCH 544/601] {chem}[iomkl/2021a] OpenMolcas v21.06

---
 .../GlobalArrays-5.8-iomkl-2021a.eb           | 24 ++++++++++
 .../h/HDF5/HDF5-1.10.7-iompi-2021a.eb         | 22 +++++++++
 .../OpenMolcas-21.06-iomkl-2021a.eb           | 46 +++++++++++++++++++
 3 files changed, 92 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb
 create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
 create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb

diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb
new file mode 100644
index 00000000000..6f35fb227fb
--- /dev/null
+++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb
@@ -0,0 +1,24 @@
+easyblock = 'ConfigureMake'
+
+name = 'GlobalArrays'
+version = '5.8'
+
+homepage = 'https://hpc.pnl.gov/globalarrays'
+description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model"
+
+toolchain = {'name': 'iomkl', 'version': '2021a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/%(name)s/ga/releases/download/']
+sources = ['v%(version)s/ga-%(version)s.tar.gz']
+checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac']
+
+configopts = ' --with-mpi --enable-i8 --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64" --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl" --with-mpi-ts'
+
+
+sanity_check_paths = {
+    'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
new file mode 100644
index 00000000000..2f1d4b6ddb6
--- /dev/null
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
@@ -0,0 +1,22 @@
+name = 'HDF5'
+version = '1.10.7'
+
+homepage = 'https://portal.hdfgroup.org/display/support'
+description = """HDF5 is a data model, library, and file format for storing and managing data.
+ It supports an unlimited variety of datatypes, and is designed for flexible
+ and efficient I/O and for high volume and complex data."""
+
+toolchain = {'name': 'iompi', 'version': '2021a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15']
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Szip', '2.1.1'),
+]
+
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb
new file mode 100644
index 00000000000..2de233814bf
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb
@@ -0,0 +1,46 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenMolcas'
+version = '21.06'
+
+homepage = 'https://gitlab.com/Molcas/OpenMolcas'
+description = "OpenMolcas is a quantum chemistry software package"
+
+toolchain = {'name': 'iomkl', 'version': '2021a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://gitlab.com/Molcas/%(name)s/-/archive/v%(version)s/']
+sources = ['%(name)s-v%(version)s.tar.gz']
+patches = ['%(name)s-21.06_mcpdft_deps.patch']
+checksums = [
+    '54cf989c1e0fcb7e8927f0c64fe356b300bf3537e4868356eea47105a8a06e3a',  # %(name)s-v21.06.tar.gz
+    '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a',  # %(name)s-21.06_mcpdft_deps.patch
+]
+
+builddependencies = [
+    ('CMake', '3.20.1'),
+]
+dependencies = [
+    ('GlobalArrays', '5.8'),
+    ('HDF5', '1.10.7'),
+    ('Python', '3.9.5'),
+]
+
+preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS'
+configopts = "-DLINALG=MKL -DMKLROOT=$MKLROOT -DMPI=ON -DOPENMP=ON -DGA=ON -DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON"
+
+
+sanity_check_paths = {
+    'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.so', 'sbin/help_basis', 'pymolcas'],
+    'dirs': ['data/', 'basis_library/'],
+}
+
+modextrapaths = {'PATH': ''}
+
+modextravars = {
+    'MOLCAS': '%(installdir)s',
+    'MOLCAS_DRIVER': '%(installdir)s/pymolcas',
+    'MOLCAS_SOURCE': '%(installdir)s',
+}
+
+moduleclass = 'chem'

From 93abeea1a6a862309775c83d83d4f4808afd3fec Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 May 2023 21:25:57 +0200
Subject: [PATCH 545/601] shorten source URL in HDF5 easyconfig by using 'hdf5'
 instead of '%(namelower)s'

---
 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
index 2f1d4b6ddb6..8e71c233455 100644
--- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
@@ -9,7 +9,7 @@ description = """HDF5 is a data model, library, and file format for storing and
 toolchain = {'name': 'iompi', 'version': '2021a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15']
 

From 51a4637435ab2437ea105ca5163486f78ef33de9 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <Balazs.Hajgato@UGent.be>
Date: Tue, 16 May 2023 21:31:46 +0200
Subject: [PATCH 546/601] fix line lengths

---
 .../g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb     | 10 ++++++++--
 .../easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb      |  4 ++--
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb
index 6f35fb227fb..e462c994af7 100644
--- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb
+++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb
@@ -13,11 +13,17 @@ source_urls = ['https://github.com/%(name)s/ga/releases/download/']
 sources = ['v%(version)s/ga-%(version)s.tar.gz']
 checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac']
 
-configopts = ' --with-mpi --enable-i8 --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64" --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl" --with-mpi-ts'
+configopts = ' --with-mpi --enable-i8 '
+configopts += '--with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64" '
+configopts += '--with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 '
+configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"'
+# select armci network as (Comex) MPI-1 two-sided
+configopts += ' --with-mpi-ts'
 
 
 sanity_check_paths = {
-    'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'],
+    'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a',
+              'lib/libcomex.a', 'lib/libga.a'],
     'dirs': ['include'],
 }
 
diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
index 2f1d4b6ddb6..2d9b79ce8c6 100644
--- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
@@ -9,10 +9,10 @@ description = """HDF5 is a data model, library, and file format for storing and
 toolchain = {'name': 'iompi', 'version': '2021a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s'
+               '-%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15']
-
 dependencies = [
     ('zlib', '1.2.11'),
     ('Szip', '2.1.1'),

From 24daaf14698edbd3b92e46a0c7802b6c86bedff9 Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <Balazs.Hajgato@UGent.be>
Date: Tue, 16 May 2023 21:36:42 +0200
Subject: [PATCH 547/601] fix line lengths2

---
 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
index 2d9b79ce8c6..31678f0dd6d 100644
--- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
@@ -9,8 +9,7 @@ description = """HDF5 is a data model, library, and file format for storing and
 toolchain = {'name': 'iompi', 'version': '2021a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s'
-               '-%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/hdf-%(version_major_minor)s/hdf-%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15']
 dependencies = [

From a74f24b47fde8350ae6a8ed33ad5486f877e73bc Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <Balazs.Hajgato@UGent.be>
Date: Tue, 16 May 2023 21:39:36 +0200
Subject: [PATCH 548/601] fix line lengths3

---
 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
index 31678f0dd6d..2b0187340e2 100644
--- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
+++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb
@@ -9,7 +9,7 @@ description = """HDF5 is a data model, library, and file format for storing and
 toolchain = {'name': 'iompi', 'version': '2021a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/hdf-%(version_major_minor)s/hdf-%(version)s/src']
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
 sources = [SOURCELOWER_TAR_GZ]
 checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15']
 dependencies = [

From 7ae58b8b24f94f0a56b491a5c3fe2e8ca16a27e9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 May 2023 21:39:57 +0200
Subject: [PATCH 549/601] adding easyconfigs: GapFiller-2.1.2-GCC-11.3.0.eb

---
 .../g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb | 35 +++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb

diff --git a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb
new file mode 100644
index 00000000000..8e6de771d67
--- /dev/null
+++ b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'GapFiller'
+version = '2.1.2'
+
+homepage = 'https://sourceforge.net/projects/gapfiller'
+description = """GapFiller is a seed-and-extend local assembler to fill the gap within paired reads.
+ It can be used for both DNA and RNA and it has been tested on Illumina data."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+toolchainopts = {'cstd': 'c++11', 'extra_cxxflags': '-fpermissive'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['a4c5235b1ee17e277d08cc945dbfa05af084559e546a2b7f15c9c1b703f4b237']
+
+dependencies = [
+    ('Boost', '1.79.0'),
+    ('zlib', '1.2.12'),
+]
+
+buildopts = 'bin_PROGRAMS=GapFiller '
+buildopts += 'GapFiller_CFLAGS="$CFLAGS $LDFLAGS -lz" GapFiller_CXXFLAGS="$CXXFLAGS $LDFLAGS -lz"'
+installopts = 'bin_PROGRAMS=GapFiller '
+
+postinstallcmds = ["cp -a README %(installdir)s"]
+
+sanity_check_paths = {
+    'files': ['bin/GapFiller', 'README'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["GapFiller --help"]
+
+moduleclass = 'bio'

From 28ba52b7b25cd4dc91db332f18419f20775af5d8 Mon Sep 17 00:00:00 2001
From: Victor Lopez <victor.lopez@bsc.es>
Date: Mon, 15 May 2023 16:28:51 +0200
Subject: [PATCH 550/601] Add dlb v3.3.1

---
 .../d/dlb/dlb-3.3.1-gompi-2022a.eb            | 35 +++++++++++++++++++
 .../d/dlb/dlb-3.3.1-iimpi-2022a.eb            | 35 +++++++++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb
 create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb

diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb
new file mode 100644
index 00000000000..2f86924aff4
--- /dev/null
+++ b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb
@@ -0,0 +1,35 @@
+# vim: set syntax=python:
+easyblock = 'ConfigureMake'
+
+name = 'dlb'
+version = '3.3.1'
+
+description = """
+DLB is a dynamic library designed to speed up HPC hybrid applications (i.e.,
+two levels of parallelism) by improving the load balance of the outer level of
+parallelism (e.g., MPI) by dynamically redistributing the computational
+resources at the inner level of parallelism (e.g., OpenMP). at run time.
+"""
+homepage = 'https://pm.bsc.es/dlb/'
+docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/']
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+builddependencies = [('Python', '3.10.4', '-bare')]
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['https://pm.bsc.es/ftp/dlb/releases']
+
+checksums = ['1b245acad80b03eb83e815fd59dcfc598cfddd899de4504cf6a9572fe5359f40']
+
+configopts = '--with-mpi'
+
+sanity_check_paths = {
+    'files': [
+        'bin/dlb',
+        'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT,
+        'lib64/libdlb.%s' % SHLIB_EXT
+    ],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb
new file mode 100644
index 00000000000..7d1205a8d95
--- /dev/null
+++ b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb
@@ -0,0 +1,35 @@
+# vim: set syntax=python:
+easyblock = 'ConfigureMake'
+
+name = 'dlb'
+version = '3.3.1'
+
+description = """
+DLB is a dynamic library designed to speed up HPC hybrid applications (i.e.,
+two levels of parallelism) by improving the load balance of the outer level of
+parallelism (e.g., MPI) by dynamically redistributing the computational
+resources at the inner level of parallelism (e.g., OpenMP). at run time.
+"""
+homepage = 'https://pm.bsc.es/dlb/'
+docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/']
+
+toolchain = {'name': 'iimpi', 'version': '2022a'}
+builddependencies = [('Python', '3.10.4', '-bare')]
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['https://pm.bsc.es/ftp/dlb/releases']
+
+checksums = ['1b245acad80b03eb83e815fd59dcfc598cfddd899de4504cf6a9572fe5359f40']
+
+configopts = '--with-mpi'
+
+sanity_check_paths = {
+    'files': [
+        'bin/dlb',
+        'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT,
+        'lib64/libdlb.%s' % SHLIB_EXT
+    ],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'

From f9de626dc68fdb364dd3058c894352ded6009f02 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Thu, 18 May 2023 15:55:18 +0200
Subject: [PATCH 551/601] removing version suffix

---
 .../a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb        | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
index aa1f8921915..7efa2268907 100644
--- a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
+++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
@@ -3,7 +3,6 @@ easyblock = 'PackedBinary'
 name = 'Annocript'
 version = '2.0'
 local_commit = '84fd67b'
-versionsuffix = '-Python-%(pyver)s'
 
 homepage = 'https://github.com/frankMusacchia/Annocript'
 description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes.

From cbb7198078f2b773b244683b049fa9f8b3e2fb05 Mon Sep 17 00:00:00 2001
From: deniskristak <35582739+deniskristak@users.noreply.github.com>
Date: Thu, 18 May 2023 16:08:32 +0200
Subject: [PATCH 552/601] Delete Annocript-2.0-foss-2022a-Python-3.10.4.eb

removed easyconfig with versionsuffix
---
 .../Annocript-2.0-foss-2022a-Python-3.10.4.eb | 76 -------------------
 1 file changed, 76 deletions(-)
 delete mode 100644 easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb

diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
deleted file mode 100644
index 7efa2268907..00000000000
--- a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb
+++ /dev/null
@@ -1,76 +0,0 @@
-easyblock = 'PackedBinary'
-
-name = 'Annocript'
-version = '2.0'
-local_commit = '84fd67b'
-
-homepage = 'https://github.com/frankMusacchia/Annocript'
-description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes.
- It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division
- adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways.
- Annocript also gives information about the longest ORF and the non-coding potential using external software.
- Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology
- and sequence features. """
-
-toolchain = {'name': 'foss', 'version': '2022a'}
-
-source_urls = ['https://github.com/frankMusacchia/Annocript/archive']
-sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
-patches = [
-    'annocript_fix_paths.patch',
-    'annocript_no_background.patch',
-]
-checksums = [
-    {'Annocript-2.0.tar.gz': '151dec3a390826fd2bcc7d794a9565535702dfc9c4672842e825a9fcf21406d9'},
-    {'annocript_fix_paths.patch': '95359e335a6a992f5f269e8f199c9df92d765f7ff41890298acead12d562685c'},
-    {'annocript_no_background.patch': 'ca02c2b02b7574c25128c9a4ce2b69a13a0bb2b409efd2ea63562053bf2e2c57'},
-]
-
-dependencies = [
-    ('Compress-Raw-Zlib', '2.202'),
-    ('Python', '3.10.4'),
-    ('Perl', '5.34.1'),
-    ('BioPerl', '1.7.8'),
-    ('R', '4.2.1'),
-    ('CPC2', '1.0.1'),
-    ('BLAST+', '2.13.0'),
-    ('LIBSVM', '3.30'),
-    ('MariaDB', '10.9.3'),
-    ('DBD-mysql', '4.050'),
-]
-
-postinstallcmds = [
-    # Extract dna2pep to annocript's bin folder, set permissions.
-    # It is just a series Python scripts and I'm not building it as a standalone dependency, as sources for this SW
-    # are not available elsewhere than in the Annocript repository anyway.
-    "mkdir %(installdir)s/bin ",
-    "cp %(builddir)s/Annocript-*/DL_PROGRAMS/dna2pep-1.1.tar.gz %(installdir)s/bin ",
-    "cd %(installdir)s/bin && tar -zxvf dna2pep-1.1.tar.gz ",
-    "rm %(installdir)s/bin/dna2pep-1.1.tar.gz && chmod 755 %(installdir)s/bin/dna2pep-1.1/dna2pep.py ",
-    # extract annocript itself
-    'mv %(installdir)s/annocript.pl %(installdir)s/bin/',
-    'sed -i -e "1s|#!.*$|#!/usr/bin/env perl|g" %(installdir)s/bin/annocript.pl',
-    'chmod a+rx %(installdir)s/bin/annocript.pl',
-]
-
-exts_defaultclass = 'PerlModule'
-exts_filter = ("perldoc -lm %(ext_name)s ", "")
-
-exts_list = [
-    ('CGI', '4.43', {
-        'source_tmpl': 'CGI-4.43.tar.gz',
-        'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'],
-        'checksums': ['14b94f9df6e48fc26ebc4fa1e01a7b534cbc1611028a49028f9ac9d8ca27b734'],
-    }),
-]
-
-modextrapaths = {'PERL5LIB': ['', 'lib/perl5/site_perl/%(perlver)s/']}
-
-sanity_check_paths = {
-    'files': ['bin/annocript.pl'],
-    'dirs': [],
-}
-
-sanity_check_commands = ['annocript.pl --help']
-
-moduleclass = 'bio'

From 682dba8893da014588029b97179fca8078818b0f Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 19 May 2023 06:49:23 +0000
Subject: [PATCH 553/601] Adding make 4.3 as build-dependency for
 OpenBLAS-0.3.15-GCC-10.3.0

---
 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb
index 3b8d83f4116..f3bb9483823 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb
@@ -28,7 +28,7 @@ checksums = [
     # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch
     'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971',
 ]
-
+builddependencies = [('make', '4.3')]
 # extensive testing can be enabled by uncommenting the line below
 # runtest = 'PATH=.:$PATH lapack-timing'
 

From e096c0fec8037599cd1e88cc006b0d881dac8bf5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 19 May 2023 11:27:12 +0200
Subject: [PATCH 554/601] consistently use make 4.3 as build dependency for
 recent OpenBLAS versions

---
 .../m/make/make-4.3-GCCcore-12.2.0.eb         | 29 +++++++++++++++++++
 .../o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb  |  4 +++
 .../o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb  |  6 +++-
 .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb  |  4 +++
 .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb  |  1 +
 .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb  |  1 +
 .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb  |  1 +
 .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb  |  1 +
 .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb |  4 +++
 .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb  |  1 +
 .../o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb    |  4 +++
 11 files changed, 55 insertions(+), 1 deletion(-)
 create mode 100644 easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb

diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb
new file mode 100644
index 00000000000..2d7194c6354
--- /dev/null
+++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'make'
+version = '4.3'
+
+homepage = 'https://www.gnu.org/software/make/make.html'
+description = "GNU version of make utility"
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19']
+
+builddependencies = [('binutils', '2.39')]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"]
+
+sanity_check_paths = {
+    'files': ['bin/gmake', 'bin/make'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "gmake --help",
+    "make --help",
+]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb
index c98d769985e..48333ab642d 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb
@@ -31,6 +31,10 @@ checksums = [
     '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7',
 ]
 
+builddependencies = [
+    ('make', '4.3'),
+]
+
 # extensive testing can be enabled by uncommenting the line below
 # runtest = 'PATH=.:$PATH lapack-timing'
 
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb
index f3bb9483823..13b731bc6d1 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb
@@ -28,7 +28,11 @@ checksums = [
     # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch
     'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971',
 ]
-builddependencies = [('make', '4.3')]
+
+builddependencies = [
+    ('make', '4.3'),
+]
+
 # extensive testing can be enabled by uncommenting the line below
 # runtest = 'PATH=.:$PATH lapack-timing'
 
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb
index ae8fd51485e..a7984cac146 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb
@@ -25,6 +25,10 @@ checksums = [
     'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971',
 ]
 
+builddependencies = [
+    ('make', '4.3'),
+]
+
 # extensive testing can be enabled by uncommenting the line below
 # runtest = 'PATH=.:$PATH lapack-timing'
 
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb
index c4b29c67422..1df506125c2 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb
@@ -39,6 +39,7 @@ checksums = [
 ]
 
 builddependencies = [
+    ('make', '4.3'),
     # required by LAPACK test suite
     ('Python', '3.9.6', '-bare'),
 ]
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb
index 762a9558bfb..e00c62b1089 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb
@@ -36,6 +36,7 @@ checksums = [
 ]
 
 builddependencies = [
+    ('make', '4.3'),
     # required by LAPACK test suite
     ('Python', '3.9.6', '-bare'),
 ]
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb
index 98f44c83e7c..ad53aa70e6b 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb
@@ -34,6 +34,7 @@ checksums = [
 ]
 
 builddependencies = [
+    ('make', '4.3'),
     # required by LAPACK test suite
     ('Python', '3.9.6', '-bare'),
 ]
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb
index 4496c0bc5b3..c00bedf7a63 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb
@@ -34,6 +34,7 @@ checksums = [
 ]
 
 builddependencies = [
+    ('make', '4.3'),
     # required by LAPACK test suite
     ('Python', '3.10.4', '-bare'),
 ]
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb
index 39645058d21..7b49821c348 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb
@@ -33,6 +33,10 @@ checksums = [
     {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'},
 ]
 
+builddependencies = [
+    ('make', '4.3'),
+]
+
 # extensive testing can be enabled by uncommenting the line below
 # runtest = 'PATH=.:$PATH lapack-timing'
 
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb
index b0244cb98ce..274aeeec351 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb
@@ -34,6 +34,7 @@ checksums = [
 ]
 
 builddependencies = [
+    ('make', '4.3'),
     # required by LAPACK test suite
     ('Python', '3.10.8', '-bare'),
 ]
diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb
index c390c260b68..0e4b7e6439e 100644
--- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb
+++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb
@@ -36,6 +36,10 @@ checksums = [
     '9210a94ae418b4ce6d9f7fab4e00dd3155451f5ef3769536a4d954a2149ca733',  # OpenBLAS-0.3.9_fix-lapack_h.patch
 ]
 
+builddependencies = [
+    ('make', '4.3'),
+]
+
 # extensive testing can be enabled by uncommenting the line below
 # runtest = 'PATH=.:$PATH lapack-timing'
 

From bf7999b6dc64d25045d9dfcfac2369a0748d4389 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Fri, 19 May 2023 15:04:33 +0200
Subject: [PATCH 555/601] fix moduleclass

---
 .../turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb
index 890702f6e8a..0fa522cb25d 100644
--- a/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb
+++ b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb
@@ -32,4 +32,4 @@ sanity_check_paths = {
     'dirs': [],
 }
 
-moduleclass = 'bio'
+moduleclass = 'cae'

From 5304e84215f8e70751c41955f95d6136b5b7f9ad Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Fri, 19 May 2023 15:20:09 +0000
Subject: [PATCH 556/601] adding easyconfigs:
 MRPRESSO-1.0-20230502-foss-2022a.eb

---
 .../MRPRESSO-1.0-20230502-foss-2022a.eb       | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb

diff --git a/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb
new file mode 100644
index 00000000000..710f1feccad
--- /dev/null
+++ b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb
@@ -0,0 +1,28 @@
+easyblock = 'RPackage'
+
+name = 'MRPRESSO'
+# In spite of the repo name, everything else refers to MRPRESSO
+local_commit = 'cece763'
+# see DESCRIPTION to determine version,
+# but also take date of last commit into account (since version isn't always bumped)
+version = '1.0-20230502'
+
+homepage = 'https://github.com/rondolab/MR-PRESSO'
+description = "Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) method.."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/rondolab/MR-PRESSO/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['f6c464f239eaf6341ac19bde272b3b1c0700013c32bcf480c1a2f18d177b630f']
+
+dependencies = [
+    ('R', '4.2.1'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+moduleclass = 'bio'

From 19f6f48cb13ba989baead6c764bb793721f87c02 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 18:21:44 +0200
Subject: [PATCH 557/601] adding easyconfigs: pkgconf-1.9.5-GCCcore-12.3.0.eb

---
 .../p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..716412bd025
--- /dev/null
+++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'pkgconf'
+version = '1.9.5'
+
+homepage = 'https://github.com/pkgconf/pkgconf'
+
+description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries.
+ It is similar to pkg-config from freedesktop.org."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://distfiles.dereferenced.org/pkgconf/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6466efd2e38c4c0ac5de4e345f0dc6dad57e689efb08c31f2a71547683d20dc7']
+
+builddependencies = [('binutils', '2.40')]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"]
+
+sanity_check_paths = {
+    'files': ['bin/pkg-config', 'bin/pkgconf'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    "pkg-config --help",
+    "pkgconf --help",
+]
+
+moduleclass = 'devel'

From 7fb2e4076754e77b825ab4fb2879c9f55ab823ff Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 18:24:41 +0200
Subject: [PATCH 558/601] adding easyconfigs: libtool-2.4.7-GCCcore-12.3.0.eb

---
 .../l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..d3c279ea343
--- /dev/null
+++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'libtool'
+version = '2.4.7'
+
+homepage = 'https://www.gnu.org/software/libtool'
+
+description = """
+ GNU libtool is a generic library support script. Libtool hides the complexity
+ of using shared libraries behind a consistent, portable interface.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('M4', '1.4.19'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT],
+    'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'],
+}
+
+moduleclass = 'lib'

From 36c9729c22bbe435eeb5cfad59ea5a2a51c53d4e Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Fri, 19 May 2023 16:38:51 +0000
Subject: [PATCH 559/601] adding easyconfigs:
 LIANA-0.1.11-foss-2022a-R-4.2.1.eb

---
 .../LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb  | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb

diff --git a/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb
new file mode 100644
index 00000000000..2584ae7e67f
--- /dev/null
+++ b/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb
@@ -0,0 +1,56 @@
+easyblock = 'Bundle'
+
+name = 'LIANA'
+version = '0.1.11'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://saezlab.github.io/liana/'
+description = """LIANA: a LIgand-receptor ANalysis frAmework. LIANA enables the use of any 
+ combination of ligand-receptor methods and resources, and their consensus.""" 
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+    'https://cran.r-project.org/src/contrib/',  # current version of packages
+    'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    'https://bioconductor.org/packages/release/bioc/src/contrib/'  # contrib for Bioconductor packages
+]
+
+dependencies = [
+    ('R', '4.2.1'),
+    ('R-bundle-Bioconductor', '3.15', versionsuffix),
+]
+
+exts_defaultclass = 'RPackage'
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    'source_urls': source_urls,
+}
+
+exts_list = [
+    ('rlang', '1.0.4', {
+        'checksums': ['1fb789d46c6a855ce37eba63c353b85aa600c4a2a7ca6075f2632540b42a8696'],
+    }),
+    ('tidyselect', '1.2.0', {
+        'checksums': ['538d26b727e37d618e2efd3b00836048f103112a03e6994bf07a02392e269e3b'],
+    }),
+    ('OmnipathR', '3.8.0', {
+        'checksums': ['0e12ea562e135a8c670b5b4ec4000463c9ee12bd6d957bfcc2db36b5ecd85664'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/saezlab/liana/archive/refs/tags/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['fd866f4b66ee3d98c63f43d5437527c541ce624fe303a2ee2fdb729770afa91e'],
+        'modulename': 'liana'
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['liana'],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'bio'

From a535e134c2c0fb39c4481853bc4ef2af35c7bf97 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 19:00:43 +0200
Subject: [PATCH 560/601] adding easyconfigs: libxml2-2.11.4-GCCcore-12.3.0.eb,
 gettext-0.21.1-GCCcore-12.3.0.eb

---
 .../gettext/gettext-0.21.1-GCCcore-12.3.0.eb  | 37 +++++++++++++++++++
 .../libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb  | 27 ++++++++++++++
 2 files changed, 64 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..d3c0439ba9c
--- /dev/null
+++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'gettext'
+version = '0.21.1'
+
+homepage = 'https://www.gnu.org/software/gettext/'
+description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may
+build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools
+and documentation"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('libxml2', '2.11.4'),
+    ('ncurses', '6.4'),
+]
+
+configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2'
+
+sanity_check_paths = {
+    'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT,
+              'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = [
+    "gettext --help",
+    "msginit --help",
+]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..13845741e03
--- /dev/null
+++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb
@@ -0,0 +1,27 @@
+name = 'libxml2'
+version = '2.11.4'
+
+homepage = 'http://xmlsoft.org/'
+
+description = """
+ Libxml2 is the XML C parser and toolchain developed for the Gnome project
+ (but usable outside of the Gnome platform).
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['737e1d7f8ab3f139729ca13a2494fd17bf30ddb4b7a427cf336252cab57f57f7']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('XZ', '5.4.2'),
+    ('zlib', '1.2.13'),
+]
+
+moduleclass = 'lib'

From ce52564c3c53585b977851c30a5e85defffb25d0 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 19:03:29 +0200
Subject: [PATCH 561/601] adding easyconfigs: libpng-1.6.39-GCCcore-12.3.0.eb

---
 .../l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1bd630a9c13
--- /dev/null
+++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'libpng'
+version = '1.6.39'
+
+homepage = 'http://www.libpng.org/pub/png/libpng.html'
+
+description = "libpng is the official PNG reference library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['af4fb7f260f839919e5958e5ab01a275d4fe436d45442a36ee62f73e5beb75ba']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('zlib', '1.2.13')]
+
+local_majminver = '%(version_major)s%(version_minor)s'
+
+sanity_check_paths = {
+    'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h',
+              'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT,
+              'lib/libpng%s.a' % local_majminver,
+              'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)],
+    'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'],
+}
+
+moduleclass = 'lib'

From c6fa45e029b3060ea23dbd06a3a007fb4f1506fa Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 19:12:28 +0200
Subject: [PATCH 562/601] adding easyconfigs: zstd-1.5.5-GCCcore-12.3.0.eb,
 gzip-1.12-GCCcore-12.3.0.eb, lz4-1.9.4-GCCcore-12.3.0.eb

---
 .../g/gzip/gzip-1.12-GCCcore-12.3.0.eb        | 29 +++++++++++++
 .../l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb         | 30 ++++++++++++++
 .../z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb       | 41 +++++++++++++++++++
 3 files changed, 100 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..917a7468794
--- /dev/null
+++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'gzip'
+version = '1.12'
+
+homepage = 'https://www.gnu.org/software/gzip/'
+description = "gzip (GNU zip) is a popular data compression program as a replacement for compress"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch']
+checksums = [
+    '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085',  # gzip-1.12.tar.gz
+    # gzip-1.12_fix-gnulib-strndup-redeclaration.patch
+    '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4',
+]
+
+builddependencies = [('binutils', '2.40')]
+
+sanity_check_paths = {
+    'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"],
+    'dirs': [],
+}
+
+sanity_check_commands = [True, ('gzip', '--version')]
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1386e6dc615
--- /dev/null
+++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'lz4'
+version = '1.9.4'
+
+homepage = 'https://lz4.github.io/lz4/'
+description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core.
+ It features an extremely fast decoder, with speed in multiple GB/s per core."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+github_account = '%(name)s'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b']
+
+builddependencies = [('binutils', '2.40')]
+
+skipsteps = ['configure']
+
+installopts = "PREFIX=%(installdir)s"
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"],
+    'dirs': ["lib/pkgconfig"]
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..dda0d74b174
--- /dev/null
+++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'zstd'
+version = '1.5.5'
+
+homepage = 'https://facebook.github.io/zstd'
+description = """Zstandard is a real-time compression algorithm, providing high compression ratios.
+ It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder.
+ It also offers a special mode for small data, called dictionary compression, and can create dictionaries
+ from any sample set."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+github_account = 'facebook'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['98e9c3d949d1b924e28e01eccb7deed865eefebf25c2f21c702e5cd5b63b85e1']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('gzip', '1.12'),
+    ('XZ', '5.4.2'),
+    ('lz4', '1.9.4'),
+]
+
+skipsteps = ['configure']
+
+runtest = 'check'
+
+installopts = "PREFIX=%(installdir)s"
+
+sanity_check_paths = {
+    'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"],
+    'dirs': ["lib/pkgconfig"]
+}
+
+moduleclass = 'lib'

From b78b8c46ec1b290b3f5bac4bfe8a4d3c8d35c726 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 19:21:39 +0200
Subject: [PATCH 563/601] adding easyconfigs:
 libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb, NASM-2.16.01-GCCcore-12.3.0.eb

---
 .../libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb   | 42 +++++++++++++++++++
 .../n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb     | 25 +++++++++++
 2 files changed, 67 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..db21ae7cbeb
--- /dev/null
+++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'CMakeMake'
+
+name = 'libjpeg-turbo'
+version = '2.1.5.1'
+
+homepage = 'https://sourceforge.net/projects/libjpeg-turbo/'
+
+description = """
+ libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to
+ accelerate baseline JPEG compression and decompression. libjpeg is a library
+ that implements JPEG image encoding, decoding and transcoding.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['2fdc3feb6e9deb17adec9bafa3321419aa19f8f4e5dea7bf8486844ca22207bf']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('NASM', '2.16.01'),
+]
+
+configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1'
+
+runtest = "test"
+
+sanity_check_paths = {
+    'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom',
+              'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a',
+              'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a',
+              'lib/libturbojpeg.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..5c1bbfafd36
--- /dev/null
+++ b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'NASM'
+version = '2.16.01'
+
+homepage = 'https://www.nasm.us/'
+
+description = """NASM: General-purpose x86 assembler"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['35b6ad2ee048d41c4779f073f3efca7762a822b7d2d4ef4e8df24cf65747bb2e']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/nasm'],
+    'dirs': [],
+}
+
+moduleclass = 'lang'

From 51cfc490643aa93ead80de5defef6b76cffd4c53 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 20:18:31 +0200
Subject: [PATCH 564/601] adding easyconfigs:
 double-conversion-3.3.0-GCCcore-12.3.0.eb

---
 .../double-conversion-3.3.0-GCCcore-12.3.0.eb | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..66e54112889
--- /dev/null
+++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'double-conversion'
+version = '3.3.0'
+
+homepage = 'https://github.com/google/double-conversion'
+description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/google/%(name)s/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['04ec44461850abbf33824da84978043b22554896b552c5fd11a9c5ae4b4d296e']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+separate_build_dir = True
+
+build_type = 'Release'
+
+# Build static lib, static lib with -fPIC and shared lib
+configopts = [
+    '',
+    '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a',
+    '-DBUILD_SHARED_LIBS=ON'
+]
+
+sanity_check_paths = {
+    'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion',
+                                                             'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] +
+             ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From 46e712d814a7dd6e26ad1fad7c4436c3dcb97889 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 20:26:48 +0200
Subject: [PATCH 565/601] adding easyconfigs: mold-1.11.0-GCCcore-12.3.0.eb

---
 .../m/mold/mold-1.11.0-GCCcore-12.3.0.eb      | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..256cc29ec4c
--- /dev/null
+++ b/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'CMakeMake'
+
+name = 'mold'
+version = '1.11.0'
+
+homepage = 'https://github.com/rui314/mold'
+description = "mold is a high-performance drop-in replacement for existing Unix linkers."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/rui314/mold/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['99318eced81b09a77e4c657011076cc8ec3d4b6867bd324b8677974545bc4d6f']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT],
+    'dirs': ['share/man'],
+}
+
+sanity_check_commands = [
+    "mold --help",
+    "mold --run gcc -v",
+]
+
+moduleclass = 'tools'

From 82073c29e1ad9b149862c41915b3af592c395003 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 20:55:32 +0200
Subject: [PATCH 566/601] adding easyconfigs: NSS-3.89.1-GCCcore-12.3.0.eb,
 NSPR-4.35-GCCcore-12.3.0.eb

---
 .../n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb        | 30 +++++++++
 .../n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb        | 61 +++++++++++++++++++
 2 files changed, 91 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..a5ee868d241
--- /dev/null
+++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'NSPR'
+version = '4.35'
+
+homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR'
+description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level
+ and libc-like functions."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f']
+
+builddependencies = [('binutils', '2.40')]
+
+configopts = "--disable-debug --enable-optimize --enable-64bit"
+
+sanity_check_paths = {
+    'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT,
+              'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT,
+              'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT,
+              'lib/pkgconfig/nspr.pc'],
+    'dirs': ['include/nspr'],
+}
+
+sanity_check_commands = ["nspr-config --version"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..7b9beb5c086
--- /dev/null
+++ b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb
@@ -0,0 +1,61 @@
+easyblock = 'MakeCp'
+
+name = 'NSS'
+version = '3.89.1'
+
+homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS'
+description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development
+ of security-enabled client and server applications."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%s_RTM/src/' % version.replace('.', '_')]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'NSS-3.39_pkgconfig.patch',
+    'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch',
+]
+checksums = [
+    {'nss-3.89.1.tar.gz': '3adaedb9e70c3c5f40603bf60a01e336190a6dbe01929d395f16b01fe84a0156'},
+    {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'},
+    {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch':
+     '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'},
+]
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('NSPR', '4.35'),
+    ('zlib', '1.2.13'),
+]
+
+# building in parallel fails
+parallel = 1
+
+# disable use of -Werror to work around compilation errors with newer glibc versions,
+# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476
+buildopts = "NSS_ENABLE_WERROR=0 "
+# fix for not being able to find header files
+buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" '
+# fix c standard causing missing functions
+buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && '
+# also install pkgconfig file (see patch)
+buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -"
+# optional testsuite (takes a long time)
+# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh "
+
+files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')]
+
+sanity_check_paths = {
+    'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'],
+    'dirs': ['include/dbm', 'include/nss'],
+}
+
+sanity_check_commands = [
+    "multinit --help",
+    "nss-config --version",
+]
+
+modextrapaths = {'CPATH': 'include/nss'}
+
+moduleclass = 'lib'

From 5c4de2bbe909eb60840c61e072fd3c6bb831e41d Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 22:26:59 +0200
Subject: [PATCH 567/601] adding easyconfigs: DBus-1.15.4-GCCcore-12.3.0.eb,
 expat-2.5.0-GCCcore-12.3.0.eb

---
 .../d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb      | 44 +++++++++++++++++++
 .../e/expat/expat-2.5.0-GCCcore-12.3.0.eb     | 31 +++++++++++++
 2 files changed, 75 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..686c369b6a7
--- /dev/null
+++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb
@@ -0,0 +1,44 @@
+easyblock = 'ConfigureMake'
+
+name = 'DBus'
+version = '1.15.4'
+
+homepage = 'https://dbus.freedesktop.org/'
+
+description = """
+ D-Bus is a message bus system, a simple way for applications to talk
+ to one another.  In addition to interprocess communication, D-Bus helps
+ coordinate process lifecycle; it makes it simple and reliable to code
+ a "single instance" application or daemon, and to launch applications
+ and daemons on demand when their services are needed.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://dbus.freedesktop.org/releases/dbus']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['bfe53d9e54a4977ec344928521b031af2e97cf78aea58f5d8e2b85ea0a80028b']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('expat', '2.5.0'),
+]
+
+configopts = '--with-systemdsystemunitdir=no '
+# disable documentation
+configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs'
+
+sanity_check_paths = {
+    'files': ['bin/dbus-%s' % x for x in
+              ['cleanup-sockets', 'daemon', 'launch', 'monitor',
+               'run-session', 'send', 'uuidgen']] +
+             ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..5cca3ac204e
--- /dev/null
+++ b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'expat'
+version = '2.5.0'
+
+homepage = 'https://libexpat.github.io'
+
+description = """Expat is an XML parser library written in C. It is a stream-oriented parser
+in which an application registers handlers for things the parser might find
+in the XML document (like start tags)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')]
+sources = [SOURCE_TAR_BZ2]
+checksums = ['6f0e6e01f7b30025fa05c85fdad1e5d0ec7fd35d9f61b22f34998de11969ff67']
+
+builddependencies = [('binutils', '2.40')]
+
+# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf.
+# Docbook2X needs XML-Parser and XML-Parser needs expat.
+# -> circular dependency. "--without-docbook" breaks this circle.
+configopts = ['--without-docbook']
+
+sanity_check_paths = {
+    'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

From e9c6e7366182578377f1bd35d79bd13912d26d9b Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 22:37:27 +0200
Subject: [PATCH 568/601] adding easyconfigs: snappy-1.1.10-GCCcore-12.3.0.eb

---
 .../s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb  | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..52a0f6777b8
--- /dev/null
+++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb
@@ -0,0 +1,37 @@
+easyblock = 'CMakeMake'
+
+name = 'snappy'
+version = '1.1.10'
+
+homepage = 'https://github.com/google/snappy'
+description = """Snappy is a compression/decompression library. It does not aim
+for maximum compression, or compatibility with any other compression library;
+instead, it aims for very high speeds and reasonable compression."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/google/snappy/archive/']
+sources = ['%(version)s.tar.gz']
+patches = [
+    '%(name)s-1.1.9_use-default-rtti.patch',
+]
+checksums = [{
+    '1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90',
+    'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d',
+}]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code
+_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF'
+configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts]
+
+sanity_check_paths = {
+    'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'],
+    'dirs': []
+}
+
+moduleclass = 'lib'

From a73725f77e872fbec77fed54979b6cd6e06522a6 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 22:39:59 +0200
Subject: [PATCH 569/601] adding easyconfigs:
 graphite2-1.3.14-GCCcore-12.3.0.eb

---
 .../graphite2-1.3.14-GCCcore-12.3.0.eb        | 27 +++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..0c6ebe10a4c
--- /dev/null
+++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'CMakeMake'
+
+name = 'graphite2'
+version = '1.3.14'
+
+homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home'
+description = """Graphite is a "smart font" system developed specifically to
+ handle the complexities of lesser-known languages of the world."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/silnrsi/graphite/archive/']
+sources = ['%(version)s.zip']
+checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gr2fonttest'] +
+             ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']],
+    'dirs': ['include/%(name)s', 'share']
+}
+
+moduleclass = 'lib'

From 6fcdebd415e78f64918bf0ab9d3317c2463677f6 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 22:51:29 +0200
Subject: [PATCH 570/601] adding easyconfigs: Doxygen-1.9.7-GCCcore-12.3.0.eb,
 libiconv-1.17-GCCcore-12.3.0.eb

---
 .../d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb | 31 +++++++++++++++++++
 .../libiconv/libiconv-1.17-GCCcore-12.3.0.eb  | 23 ++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..26007e7a823
--- /dev/null
+++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+name = 'Doxygen'
+version = '1.9.7'
+
+homepage = 'https://www.doxygen.org'
+description = """
+ Doxygen is a documentation system for C++, C, Java, Objective-C, Python,
+ IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some
+ extent D.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(namelower)s-%(version)s.src.tar.gz']
+checksums = ['87007641c38e2c392c8596f36711eb97633b984c8430f389e7bcf6323a098d94']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('Bison', '3.8.2'),
+    ('CMake', '3.26.3'),
+    ('flex', '2.6.4'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('libiconv', '1.17'),
+]
+
+configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF"
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..2f013448152
--- /dev/null
+++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb
@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'libiconv'
+version = '1.17'
+
+homepage = 'https://www.gnu.org/software/libiconv'
+description = "Libiconv converts from one character encoding to another through Unicode conversion"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313']
+
+builddependencies = [('binutils', '2.40')]
+
+sanity_check_paths = {
+    'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h',
+              'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT],
+    'dirs': ['share'],
+}
+
+moduleclass = 'lib'

From ba2fef107abce8c2f7f3b94aa0bccdfcfd554bf6 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 23:08:18 +0200
Subject: [PATCH 571/601] update snappy-1.1.10-GCCcore-12.3.0.eb: use correct
 checksums

---
 .../easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb  | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb
index 52a0f6777b8..a221f9f9ea5 100644
--- a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb
@@ -15,10 +15,10 @@ sources = ['%(version)s.tar.gz']
 patches = [
     '%(name)s-1.1.9_use-default-rtti.patch',
 ]
-checksums = [{
-    '1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90',
-    'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d',
-}]
+checksums = [
+    {'1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90'},
+    {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'},
+]
 
 builddependencies = [
     ('binutils', '2.40'),

From 3e40883aef575be4b612aa5d1cc25623e9d16680 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 19 May 2023 23:16:06 +0200
Subject: [PATCH 572/601] adding easyconfigs: JasPer-4.0.0-GCCcore-12.3.0.eb

---
 .../j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb   | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1568d4b64e4
--- /dev/null
+++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'CMakeMake'
+
+name = 'JasPer'
+version = '4.0.0'
+
+homepage = 'https://www.ece.uvic.ca/~frodo/jasper/'
+
+description = """
+ The JasPer Project is an open-source initiative to provide a free
+ software-based reference implementation of the codec specified in
+ the JPEG-2000 Part-1 standard.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'jasper-software'
+source_urls = [GITHUB_SOURCE]
+sources = ['version-%(version)s.tar.gz']
+checksums = ['977c4c2e4210f4e37313cd2232d99e73d57ab561917b3c060bcdd5e83a0a13f1']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+configopts = '-DJAS_ENABLE_DOC=OFF '
+
+sanity_check_paths = {
+    'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ['jasper --version']
+
+moduleclass = 'vis'

From 0f83fa5bc9ddb1bd1e2a60288a10c4694768336e Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 21 May 2023 13:28:56 +0200
Subject: [PATCH 573/601] adding easyconfigs: make-4.4.1-GCCcore-12.3.0.eb

---
 .../m/make/make-4.4.1-GCCcore-12.3.0.eb       | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..283fa0f57f8
--- /dev/null
+++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'make'
+version = '4.4.1'
+
+homepage = 'https://www.gnu.org/software/make/make.html'
+description = "GNU version of make utility"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3']
+
+builddependencies = [('binutils', '2.40')]
+
+postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"]
+
+sanity_check_paths = {
+    'files': ['bin/gmake', 'bin/make'],
+    'dirs': []
+}
+
+sanity_check_commands = [
+    "gmake --help",
+    "make --help",
+]
+
+moduleclass = 'devel'

From b5c1188c9c895757fdf842563ce302eeff2b8a00 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 21 May 2023 13:37:54 +0200
Subject: [PATCH 574/601] adding easyconfigs: PCRE2-10.42-GCCcore-12.3.0.eb,
 PCRE-8.45-GCCcore-12.3.0.eb

---
 .../p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb        | 45 +++++++++++++++++++
 .../p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb     | 28 ++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b0f34719345
--- /dev/null
+++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'ConfigureMake'
+
+name = 'PCRE'
+version = '8.45'
+
+homepage = 'https://www.pcre.org/'
+
+description = """
+ The PCRE library is a set of functions that implement regular expression
+ pattern matching using the same syntax and semantics as Perl 5.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [
+    SOURCEFORGE_SOURCE,
+    'https://ftp.pcre.org/pub/pcre/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.2.13'),
+]
+
+configopts = ' '.join([
+    '--enable-utf',
+    '--enable-unicode-properties',
+    '--enable-pcre16',
+    '--enable-pcre32',
+])
+
+sanity_check_paths = {
+    'files': ['bin/pcre-config', 'include/pcre.h',
+              'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'],
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..01813f20f0b
--- /dev/null
+++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'PCRE2'
+version = '10.42'
+
+homepage = 'https://www.pcre.org/'
+description = """
+ The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax
+ and semantics as Perl 5.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c33b418e3b936ee3153de2c61cc638e7e4fe3156022a5c77d0711bcbb9d64f1f']
+
+builddependencies = [('binutils', '2.40')]
+
+configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode"
+
+sanity_check_paths = {
+    'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

From df8d01fc9828b77cf5b033cdec0064a7239b1c5b Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Sun, 21 May 2023 14:03:58 +0200
Subject: [PATCH 575/601] adding easyconfigs: SQLite-3.42.0-GCCcore-12.3.0.eb,
 Tcl-8.6.13-GCCcore-12.3.0.eb, UnZip-6.0-GCCcore-12.3.0.eb,
 libffi-3.4.4-GCCcore-12.3.0.eb, libreadline-8.2-GCCcore-12.3.0.eb

---
 .../l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb   | 29 +++++++++
 .../libreadline-8.2-GCCcore-12.3.0.eb         | 41 +++++++++++++
 .../s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb  | 39 ++++++++++++
 .../t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb        | 41 +++++++++++++
 .../u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb       | 59 +++++++++++++++++++
 5 files changed, 209 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..416e3945706
--- /dev/null
+++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'libffi'
+version = '3.4.4'
+
+homepage = 'https://sourceware.org/libffi/'
+description = """The libffi library provides a portable, high level programming interface to
+ various calling conventions. This allows a programmer to call any function
+ specified by a call interface description at run-time."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+configopts = '--disable-exec-static-tramp '
+
+sanity_check_paths = {
+    'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..ade8ec67a13
--- /dev/null
+++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'libreadline'
+version = '8.2'
+
+homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html'
+description = """
+ The GNU Readline library provides a set of functions for use by applications
+ that allow users to edit command lines as they are typed in. Both Emacs and
+ vi editing modes are available. The Readline library includes additional
+ functions to maintain a list of previously-entered command lines, to recall
+ and perhaps reedit those lines, and perform csh-like history expansion on
+ previous commands.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://ftp.gnu.org/gnu/readline']
+sources = ['readline-%(version)s.tar.gz']
+checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('ncurses', '6.4'),
+]
+
+# for the termcap symbols, use EB ncurses
+buildopts = "SHLIB_LIBS='-lncurses'"
+
+sanity_check_paths = {
+    'files': ['lib/libreadline.a', 'lib/libhistory.a'] +
+             ['include/readline/%s' % x
+              for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h',
+                        'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..f3ebb9f775e
--- /dev/null
+++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'SQLite'
+version = '3.42.0'
+local_filename_version = '3420000'
+
+homepage = 'https://www.sqlite.org/'
+description = "SQLite: SQL Database Engine in a C Library"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.sqlite.org/2023/']
+sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)]
+checksums = ['7abcfd161c6e2742ca5c6c0895d1f853c940f203304a0b49da4e1eca5d088ca6']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('libreadline', '8.2'),
+    ('Tcl', '8.6.13'),
+]
+
+# enable additional APIs that provide access to meta-data about tables and queries
+# needed for GDAL when it used as a dep for QGIS
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"'
+
+sanity_check_paths = {
+    'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h',
+              'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig'],
+}
+
+sanity_check_commands = [
+    'sqlite3 --version | grep ^%(version)s',
+]
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..a85651a4106
--- /dev/null
+++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'Tcl'
+version = '8.6.13'
+
+homepage = 'https://www.tcl.tk/'
+description = """
+ Tcl (Tool Command Language) is a very powerful but easy to learn dynamic
+ programming language, suitable for a very wide range of uses, including web
+ and desktop applications, networking, administration, testing and many more.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s']
+sources = ['%(namelower)s%(version)s-src.tar.gz']
+checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"'
+
+runtest = 'test'
+
+start_dir = 'unix'
+
+postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh']
+
+sanity_check_paths = {
+    'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh',
+              'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT,
+              'lib/tclConfig.sh', 'man/man1/tclsh.1'],
+    'dirs': ['share'],
+}
+
+moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..7baea9a00a2
--- /dev/null
+++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb
@@ -0,0 +1,59 @@
+easyblock = 'ConfigureMake'
+
+name = 'UnZip'
+version = '6.0'
+
+homepage = 'http://www.info-zip.org/UnZip.html'
+description = """UnZip is an extraction utility for archives compressed
+in .zip format (also called "zipfiles"). Although highly compatible both
+with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's
+own Zip program, our primary objectives have been portability and
+non-MSDOS functionality."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://download.sourceforge.net/infozip']
+sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz']
+patches = [
+    'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch',
+]
+checksums = [
+    '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37',  # unzip60.tar.gz
+    # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch
+    '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe',
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+]
+
+skipsteps = ['configure']
+
+local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT'
+            '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD',
+            '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT']
+
+buildopts = ' '.join([
+    "-f unix/Makefile",
+    'CC="$CC"',
+    'D_USE_BZ2=-DUSE_BZIP2',
+    'L_BZ2=-lbz2',
+    'LF2="$LDFLAGS"',
+    'CF="%s"' % ' '.join(local_cf),
+    'unzips',
+])
+
+installopts = '-f unix/Makefile prefix=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/unzip', 'bin/zipinfo'],
+    'dirs': ['man/man1']
+}
+
+sanity_check_commands = ["unzip -v"]
+
+moduleclass = 'tools'

From 55792ec8404c91f3256a03474c6490dba9b59a86 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 21:21:26 +0200
Subject: [PATCH 576/601] adding easyconfigs: numactl-2.0.16-GCCcore-12.3.0.eb

---
 .../numactl/numactl-2.0.16-GCCcore-12.3.0.eb  | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..68237d4c0cc
--- /dev/null
+++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'numactl'
+version = '2.0.16'
+
+homepage = 'https://github.com/numactl/numactl'
+
+description = """
+ The numactl program allows you to run your application program on specific
+ cpu's and memory nodes. It does this by supplying a NUMA memory policy to
+ the operating system before running your program. The libnuma library provides
+ convenient ways for you to add NUMA memory policies into your own program.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/numactl/numactl/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['1b242f893af977a1d31af6ce9d6b8dafdd2d8ec3dc9207f7c2dc0d3446e7c7c8']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'],
+    'dirs': ['share/man', 'include']
+}
+
+moduleclass = 'tools'

From 7b3f7392c48bb36a9adcfeb41dc182561b5da2e8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 21:58:56 +0200
Subject: [PATCH 577/601] adding easyconfigs:
 googletest-1.13.0-GCCcore-12.3.0.eb

---
 .../googletest-1.13.0-GCCcore-12.3.0.eb       | 28 +++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..d54ca5d0453
--- /dev/null
+++ b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'googletest'
+version = '1.13.0'
+
+homepage = 'https://github.com/google/googletest'
+description = "Google's framework for writing C++ tests on a variety of platforms"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/google/googletest/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['ad7fdba11ea011c1d925b3289cf4af2c66a352e18d4c7264392fead75e919363']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+# build twice, once for static, once for shared libraries
+configopts = ['', ' -DBUILD_SHARED_LIBS=ON ']
+
+sanity_check_paths = {
+    'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main']
+              for local_ext in ['a', SHLIB_EXT]],
+    'dirs': ['include/gmock', 'include/gtest'],
+}
+
+moduleclass = 'tools'

From 19c6e6559fd80fb29b0bf9bd4e4369a598ec9dcb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 22:06:58 +0200
Subject: [PATCH 578/601] adding easyconfigs: Eigen-3.4.0-GCCcore-12.3.0.eb

---
 .../e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb     | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..dfd909ce779
--- /dev/null
+++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb
@@ -0,0 +1,21 @@
+name = 'Eigen'
+version = '3.4.0'
+
+homepage = 'https://eigen.tuxfamily.org'
+description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers,
+ and related algorithms."""
+
+# only includes header files, but requires CMake so using non-system toolchain
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626']
+
+# using CMake built with GCCcore to avoid relying on the system compiler to build it
+builddependencies = [
+    ('binutils', '2.40'),  # to make CMake compiler health check pass on old systems
+    ('CMake', '3.26.3'),
+]
+
+moduleclass = 'math'

From d82c81ac80fa462d4b66e2dd9c86c853522dd6ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 22:11:04 +0200
Subject: [PATCH 579/601] adding easyconfigs: LZO-2.10-GCCcore-12.3.0.eb,
 Brotli-1.0.9-GCCcore-12.3.0.eb, Szip-2.1.1-GCCcore-12.3.0.eb,
 Zip-3.0-GCCcore-12.3.0.eb, libdeflate-1.18-GCCcore-12.3.0.eb

---
 .../b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb   | 36 +++++++++++++++++
 .../l/LZO/LZO-2.10-GCCcore-12.3.0.eb          | 27 +++++++++++++
 .../libdeflate-1.18-GCCcore-12.3.0.eb         | 37 +++++++++++++++++
 .../s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb       | 29 ++++++++++++++
 .../z/Zip/Zip-3.0-GCCcore-12.3.0.eb           | 40 +++++++++++++++++++
 5 files changed, 169 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..36c52aae8f7
--- /dev/null
+++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'CMakeMake'
+
+name = 'Brotli'
+version = '1.0.9'
+
+homepage = 'https://github.com/google/brotli'
+description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination
+ of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio
+ comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate
+ but offers more dense compression.
+The specification of the Brotli Compressed Data Format is defined in RFC 7932."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/google/brotli/archive']
+sources = ['v%(version)s.tar.gz']
+patches = ['Brotli-%(version)s_pc_link_flags.patch']
+checksums = [
+    'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46',  # v1.0.9.tar.gz
+    '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e',  # Brotli-1.0.9_pc_link_flags.patch
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT,
+              'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["brotli --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..38c850b17e8
--- /dev/null
+++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'LZO'
+version = '2.10'
+
+homepage = 'https://www.oberhumer.com/opensource/lzo/'
+description = "Portable lossless data compression library"
+
+source_urls = [homepage + 'download/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072']
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [('binutils', '2.40')]
+
+configopts = '--enable-shared'
+
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT],
+    'dirs': ['include']
+}
+
+moduleclass = 'devel'
diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..3e44ca69301
--- /dev/null
+++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb
@@ -0,0 +1,37 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'CMakeMake'
+
+name = 'libdeflate'
+version = '1.18'
+
+homepage = 'https://github.com/ebiggers/libdeflate'
+description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+github_account = 'ebiggers'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['225d982bcaf553221c76726358d2ea139bb34913180b20823c782cede060affd']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/%(name)s-gunzip', 'bin/%(name)s-gzip',
+        'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT,
+        'include/%(name)s.h',
+    ],
+    'dirs': [],
+}
+sanity_check_commands = [
+    '%(name)s-gzip -h',
+    '%(name)s-gunzip -h',
+]
+
+moduleclass = 'system'
diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..e0a01221b9d
--- /dev/null
+++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb
@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'Szip'
+version = '2.1.1'
+
+homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/'
+
+description = """
+ Szip compression software, providing lossless compression of scientific data
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+sanity_check_paths = {
+    'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] +
+             ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..ff3257294a7
--- /dev/null
+++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb
@@ -0,0 +1,40 @@
+easyblock = 'ConfigureMake'
+
+name = 'Zip'
+version = '3.0'
+
+homepage = 'http://www.info-zip.org/Zip.html'
+description = """Zip is a compression and file packaging/archive utility.
+Although highly compatible both with PKWARE's PKZIP and PKUNZIP
+utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives
+have been portability and other-than-MSDOS functionality"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://download.sourceforge.net/infozip']
+sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz']
+checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('bzip2', '1.0.8'),
+]
+
+skipsteps = ['configure']
+
+buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 '
+buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" '
+buildopts += 'generic_gcc'
+
+installopts = '-f unix/Makefile prefix=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'],
+    'dirs': ['man/man1']
+}
+
+sanity_check_commands = ["zip --version"]
+
+moduleclass = 'tools'

From a4fa006233165c82c3f2065432db0c16e3f37a4c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 22:31:01 +0200
Subject: [PATCH 580/601] adding easyconfigs: FLAC-1.4.2-GCCcore-12.3.0.eb,
 libvorbis-1.3.7-GCCcore-12.3.0.eb, libogg-1.3.5-GCCcore-12.3.0.eb,
 libopus-1.4-GCCcore-12.3.0.eb

---
 .../f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb       | 30 +++++++++++++++++++
 .../l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb   | 25 ++++++++++++++++
 .../l/libopus/libopus-1.4-GCCcore-12.3.0.eb   | 30 +++++++++++++++++++
 .../libvorbis-1.3.7-GCCcore-12.3.0.eb         | 30 +++++++++++++++++++
 4 files changed, 115 insertions(+)
 create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..6b89c621af0
--- /dev/null
+++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'FLAC'
+version = '1.4.2'
+
+homepage = 'https://xiph.org/flac/'
+description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning
+that audio is compressed in FLAC without any loss in quality."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['e322d58a1f48d23d9dd38f432672865f6f79e73a6f9cc5a5f57fcaa83eb5a8e4']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('libogg', '1.3.5')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a',
+              'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT],
+    'dirs': ['include/FLAC', 'include/FLAC++'],
+}
+
+sanity_check_commands = ["flac --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..8d57716f577
--- /dev/null
+++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'libogg'
+version = '1.3.5'
+
+homepage = 'https://xiph.org/ogg/'
+description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org
+multimedia codecs."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/']
+sources = [SOURCELOWER_TAR_XZ]
+checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705']
+
+builddependencies = [('binutils', '2.40')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT],
+    'dirs': ['include/ogg'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..576b4556eec
--- /dev/null
+++ b/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'libopus'
+version = '1.4'
+
+homepage = 'https://www.opus-codec.org/'
+description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive
+ speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is
+ standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s
+ SILK codec and Xiph.Org’s CELT codec."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://downloads.xiph.org/releases/opus/']
+sources = ['opus-%(version)s.tar.gz']
+checksums = ['c9b32b4253be5ae63d1ff16eea06b94b5f0f2951b7a02aceef58e3a3ce49c51f']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT],
+    'dirs': ['include/opus'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..40c5f137808
--- /dev/null
+++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'libvorbis'
+version = '1.3.7'
+
+homepage = 'https://xiph.org/vorbis/'
+description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed
+audio format"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [('libogg', '1.3.5')]
+
+configopts = '--enable-static --enable-shared'
+
+sanity_check_paths = {
+    'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT],
+    'dirs': ['include/vorbis'],
+}
+
+moduleclass = 'lib'

From cdd9bee3ea98f1310ca6d5bac5753bc77236e6b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 22:39:21 +0200
Subject: [PATCH 581/601] adding easyconfigs: jbigkit-2.1-GCCcore-12.3.0.eb,
 LibTIFF-4.5.0-GCCcore-12.3.0.eb, OpenJPEG-2.5.0-GCCcore-12.3.0.eb

---
 .../j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb   | 45 +++++++++++++++++++
 .../l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb | 35 +++++++++++++++
 .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb | 42 +++++++++++++++++
 3 files changed, 122 insertions(+)
 create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b6086a98262
--- /dev/null
+++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb
@@ -0,0 +1,45 @@
+easyblock = 'MakeCp'
+
+name = 'jbigkit'
+version = '2.1'
+
+homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/'
+description = """JBIG-KIT is a software implementation of the JBIG1 data
+ compression standard (ITU-T T.82), which was designed for bi-level image
+ data, such as scanned documents."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download']
+sources = [SOURCE_TAR_GZ]
+patches = [
+    '%(name)s-%(version)s_libpath.patch',
+    '%(name)s-%(version)s_shlib.patch',
+]
+checksums = [
+    {'jbigkit-2.1.tar.gz': 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932'},
+    {'jbigkit-2.1_libpath.patch': '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce'},
+    {'jbigkit-2.1_shlib.patch': '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+]
+
+files_to_copy = [
+    (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'),
+    (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'),
+    (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libjbig85.a', 'lib/libjbig.a',
+              'bin/pbmtojbg', 'bin/jbgtopbm',
+              'include/jbig.h', 'include/jbig_ar.h',
+              ],
+    'dirs': ['bin', 'include', 'lib']
+}
+
+moduleclass = 'vis'
diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..706cc20c7dc
--- /dev/null
+++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'LibTIFF'
+version = '4.5.0'
+
+homepage = 'https://libtiff.gitlab.io/libtiff/'
+description = "tiff: Library and tools for reading and writing TIFF data files"
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://download.osgeo.org/libtiff/']
+sources = ['tiff-%(version)s.tar.gz']
+checksums = ['c7a1d9296649233979fa3eacffef3fa024d73d05d589cb622727b5b08c423464']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('XZ', '5.4.2'),
+    ('jbigkit', '2.1'),
+    ('zstd', '1.5.5'),
+    ('libdeflate', '1.18'),
+]
+
+configopts = "--enable-ld-version-script "
+configopts += '--disable-webp'
+
+sanity_check_paths = {
+    'files': ['bin/tiffinfo'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..e930df38233
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenJPEG'
+version = '2.5.0'
+
+homepage = 'https://www.openjpeg.org/'
+description = """OpenJPEG is an open-source JPEG 2000 codec written in
+ C language. It has been developed in order to promote the use of JPEG 2000,
+ a still-image compression standard from the Joint Photographic Experts Group
+ (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as
+ a JPEG 2000 Reference Software."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/uclouvain/%(namelower)s/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc.
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('libpng', '1.6.39'),
+    ('LibTIFF', '4.5.0'),
+]
+
+sanity_check_paths = {
+    'files': [
+        'bin/opj_compress',
+        'bin/opj_decompress',
+        'bin/opj_dump',
+        'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h',
+        'lib/libopenjp2.%s' % SHLIB_EXT
+    ],
+    'dirs': ['bin', 'include', 'lib'],
+}
+
+moduleclass = 'lib'

From c76c26d0faa8b6041d713b307fc1f480b1551f78 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 22:47:18 +0200
Subject: [PATCH 582/601] adding easyconfigs: OpenEXR-3.1.7-GCCcore-12.3.0.eb,
 Imath-3.1.7-GCCcore-12.3.0.eb

---
 .../i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb     | 28 ++++++++++++++
 .../o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb | 38 +++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b6497fabaeb
--- /dev/null
+++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Imath'
+version = '3.1.7'
+
+homepage = 'https://imath.readthedocs.io/en/latest/'
+description = """
+Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['bff1fa140f4af0e7f02c6cb78d41b9a7d5508e6bcdfda3a583e35460eb6d4b47']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libImath.%s' % SHLIB_EXT],
+    'dirs': ['include/Imath'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..f66f45d25c3
--- /dev/null
+++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'CMakeMake'
+
+name = 'OpenEXR'
+version = '3.1.7'
+
+homepage = 'https://www.openexr.com/'
+description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic
+ for use in computer imaging applications"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['78dbca39115a1c526e6728588753955ee75fa7f5bb1a6e238bed5b6d66f91fd7']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+dependencies = [
+    ('Imath', '3.1.7'),
+    ('zlib', '1.2.13')
+]
+
+local_libs, local_bins = [
+    ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'],
+    ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']
+]
+
+sanity_check_paths = {
+    'files': (
+        ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] +
+        ['bin/exr%s' % b for b in local_bins]
+    ),
+    'dirs': ['include/%(name)s', 'share'],
+}
+
+moduleclass = 'vis'

From 84191cff1aa331e25e687099524739f0475ab2fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 22:54:19 +0200
Subject: [PATCH 583/601] adding easyconfigs: spdlog-1.11.0-GCCcore-12.3.0.eb,
 libunwind-1.6.2-GCCcore-12.3.0.eb, utf8proc-2.8.0-GCCcore-12.3.0.eb

---
 .../libunwind-1.6.2-GCCcore-12.3.0.eb         | 32 +++++++++++++++++++
 .../s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb  | 24 ++++++++++++++
 .../utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb | 30 +++++++++++++++++
 3 files changed, 86 insertions(+)
 create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..9ca69508042
--- /dev/null
+++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'ConfigureMake'
+
+name = 'libunwind'
+version = '1.6.2'
+
+homepage = 'https://www.nongnu.org/libunwind/'
+description = """The primary goal of libunwind is to define a portable and efficient C programming interface
+ (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the
+ preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain
+ (non-local goto). The API supports both local (same-process) and remote (across-process) operation.
+ As such, the API is useful in a number of applications"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [GNU_SAVANNAH_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [
+    ('XZ', '5.4.2'),
+]
+
+preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && '
+
+sanity_check_paths = {
+    'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..72f5f9a9923
--- /dev/null
+++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb
@@ -0,0 +1,24 @@
+easyblock = 'CMakeMake'
+
+name = 'spdlog'
+version = '1.11.0'
+
+homepage = 'https://github.com/gabime/spdlog'
+description = 'Very fast, header-only/compiled, C++ logging library.'
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['ca5cae8d6cac15dae0ec63b21d6ad3530070650f68076f3a4a862ca293a858bb']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/spdlog/spdlog.h'],
+    'dirs': ['lib64/cmake', 'lib64/pkgconfig'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..74f889da933
--- /dev/null
+++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'utf8proc'
+version = '2.8.0'
+
+homepage = 'https://github.com/JuliaStrings/utf8proc'
+description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, 
+and other operations for data in the UTF-8 encoding."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a0a60a79fe6f6d54e7d411facbfcc867a6e198608f2cd992490e46f04b1bcecc']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+separate_build_dir = True
+
+configopts = ['', '-DBUILD_SHARED_LIBS=true']
+
+sanity_check_paths = {
+    'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

From 4ad0284e7ea35c1e17c439b8b8b9d6518377cf93 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 23:20:11 +0200
Subject: [PATCH 584/601] adding easyconfigs: Highway-1.0.4-GCCcore-12.3.0.eb,
 Brunsli-0.1-GCCcore-12.3.0.eb, fmt-10.0.0-GCCcore-12.3.0.eb,
 UDUNITS-2.2.28-GCCcore-12.3.0.eb, DB-18.1.40-GCCcore-12.3.0.eb,
 libevent-2.1.12-GCCcore-12.3.0.eb, elfutils-0.189-GCCcore-12.3.0.eb

---
 .../b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb   | 50 +++++++++++++++++++
 .../d/DB/DB-18.1.40-GCCcore-12.3.0.eb         | 33 ++++++++++++
 .../elfutils/elfutils-0.189-GCCcore-12.3.0.eb | 41 +++++++++++++++
 .../f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb        | 26 ++++++++++
 .../h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb | 32 ++++++++++++
 .../libevent-2.1.12-GCCcore-12.3.0.eb         | 38 ++++++++++++++
 .../UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb  | 44 ++++++++++++++++
 7 files changed, 264 insertions(+)
 create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..e9d6adbb76f
--- /dev/null
+++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb
@@ -0,0 +1,50 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Brunsli'
+version = '0.1'
+
+homepage = 'https://github.com/google/brunsli/'
+description = """Brunsli is a lossless JPEG repacking library."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/google/brunsli/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc']
+
+builddependencies = [
+    ('CMake', '3.26.3'),
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Brotli', '1.0.9'),
+    ('Highway', '1.0.4'),
+]
+
+# skip use of third_party directory, since we provide Brotli via a proper dependency
+preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && "
+
+configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"'
+
+buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include"
+
+# also install dbrunsli binary and missing libraries
+postinstallcmds = [
+    "mkdir %(installdir)s/bin",
+    "cp dbrunsli %(installdir)s/bin/",
+    "cp libbrunsli*.a %(installdir)s/lib*/",
+    "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT,
+]
+
+sanity_check_paths = {
+    'files': ['bin/dbrunsli'],
+    'dirs': ['include/brunsli', 'lib'],
+}
+
+sanity_check_commands = ['dbrunsli 2>&1 | grep Usage']
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..5d02753039b
--- /dev/null
+++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb
@@ -0,0 +1,33 @@
+name = 'DB'
+version = '18.1.40'
+
+homepage = 'https://www.oracle.com/technetwork/products/berkeleydb'
+
+description = """Berkeley DB enables the development of custom data management
+ solutions, without the overhead traditionally associated with such custom
+ projects."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+# use http to allow auto-downloading...
+source_urls = ['http://download.oracle.com/berkeley-db/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_fix_doc_install.patch']
+checksums = [
+    '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8',  # db-18.1.40.tar.gz
+    '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d',  # DB-18.1.40_fix_doc_install.patch
+]
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('OpenSSL', '1.1', '', SYSTEM)]
+
+sanity_check_paths = {
+    'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup',
+                                        'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat',
+                                        'tuner', 'upgrade', 'verify']] +
+             ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..d1d7854b68d
--- /dev/null
+++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb
@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'elfutils'
+version = '0.189'
+
+homepage = 'https://elfutils.org/'
+
+description = """
+ The elfutils project provides libraries and tools for ELF files
+ and DWARF data.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/']
+sources = [SOURCE_TAR_BZ2]
+checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8']
+
+builddependencies = [
+    ('M4', '1.4.19'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('binutils', '2.40'),
+    ('bzip2', '1.0.8'),
+    ('libarchive', '3.6.2'),
+    ('XZ', '5.4.2'),
+    ('zstd', '1.5.5'),
+]
+
+configopts = "--disable-debuginfod --disable-libdebuginfod"
+
+sanity_check_paths = {
+    'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT],
+    'dirs': []
+}
+
+sanity_check_commands = ["eu-elfcmp --help"]
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..f4b60c8afb7
--- /dev/null
+++ b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb
@@ -0,0 +1,26 @@
+easyblock = 'CMakeMake'
+
+name = 'fmt'
+version = '10.0.0'
+
+homepage = 'http://fmtlib.net/'
+description = "fmt (formerly cppformat) is an open-source formatting library."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/']
+sources = ['fmt-%(version)s.zip']
+checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libfmt.a'],
+    'dirs': ['include/fmt', 'lib/cmake'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..a05239847d3
--- /dev/null
+++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'Highway'
+version = '1.0.4'
+
+homepage = 'https://github.com/google/highway'
+
+description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same
+operation to 'lanes'."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/google/highway/archive/refs/tags/']
+sources = ['%(version)s.tar.gz']
+checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('googletest', '1.13.0'),
+]
+
+configopts = "-DHWY_SYSTEM_GTEST=ON"
+
+runtest = "test"
+
+sanity_check_paths = {
+    'files': ['lib/libhwy.a'],
+    'dirs': ['include/hwy'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..61bf17145f5
--- /dev/null
+++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'libevent'
+version = '2.1.12'
+
+homepage = 'https://libevent.org/'
+
+description = """
+ The libevent API provides a mechanism to execute a callback function when
+ a specific event occurs on a file descriptor or after a timeout has been
+ reached.  Furthermore, libevent also support callbacks due to signals or
+ regular timeouts.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/']
+sources = ['%(name)s-%(version)s-stable.tar.gz']
+checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+sanity_check_paths = {
+    'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h',
+              'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..67b179fd479
--- /dev/null
+++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb
@@ -0,0 +1,44 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University
+# Authors::   Fotis Georgatos <fotis@cern.ch>, Kenneth Hoste (Ghent University)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'UDUNITS'
+version = '2.2.28'
+
+homepage = 'https://www.unidata.ucar.edu/software/udunits/'
+description = """UDUNITS supports conversion of unit specifications between formatted and binary forms,
+ arithmetic manipulation of units, and conversion of values between compatible scales of measurement."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [
+    'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/',
+    'https://sources.easybuild.io/u/UDUNITS/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e']
+
+builddependencies = [('binutils', '2.40')]
+
+dependencies = [('expat', '2.5.0')]
+
+sanity_check_paths = {
+    'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h',
+              'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT],
+    'dirs': ['share'],
+}
+
+parallel = 1
+
+moduleclass = 'phys'

From f749b7a72fa99c110c5977d04d0bc71494c261d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 21 May 2023 23:26:57 +0200
Subject: [PATCH 585/601] Fix checksum

---
 easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb
index f4b60c8afb7..ad80d0891f9 100644
--- a/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb
@@ -11,7 +11,7 @@ toolchainopts = {'pic': True}
 
 source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/']
 sources = ['fmt-%(version)s.zip']
-checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996']
+checksums = ['4943cb165f3f587f26da834d3056ee8733c397e024145ca7d2a8a96bb71ac281']
 
 builddependencies = [
     ('binutils', '2.40'),

From 3fcda9852e1fad91992d19873e3151e6fe7ac8f6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 22 May 2023 00:27:07 +0200
Subject: [PATCH 586/601] adding easyconfigs:
 Abseil-20230125.3-GCCcore-12.3.0.eb, Blitz++-1.0.2-GCCcore-12.3.0.eb,
 groff-1.22.4-GCCcore-12.3.0.eb, json-c-0.16-GCCcore-12.3.0.eb,
 METIS-5.1.0-GCCcore-12.3.0.eb, libtirpc-1.3.3-GCCcore-12.3.0.eb,
 libxslt-1.1.38-GCCcore-12.3.0.eb, libyaml-0.2.5-GCCcore-12.3.0.eb,
 libgeotiff-1.7.1-GCCcore-12.3.0.eb, PROJ-9.2.0-GCCcore-12.3.0.eb,
 nlohmann_json-3.11.2-GCCcore-12.3.0.eb

---
 .../Abseil-20230125.3-GCCcore-12.3.0.eb       | 31 ++++++++++++
 .../b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb | 36 ++++++++++++++
 .../g/groff/groff-1.22.4-GCCcore-12.3.0.eb    | 27 ++++++++++
 .../j/json-c/json-c-0.16-GCCcore-12.3.0.eb    | 32 ++++++++++++
 .../libgeotiff-1.7.1-GCCcore-12.3.0.eb        | 36 ++++++++++++++
 .../libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb | 28 +++++++++++
 .../libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb  | 34 +++++++++++++
 .../l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb | 25 ++++++++++
 .../m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb     | 36 ++++++++++++++
 .../nlohmann_json-3.11.2-GCCcore-12.3.0.eb    | 25 ++++++++++
 .../p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb       | 49 +++++++++++++++++++
 11 files changed, 359 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..b76e53de45b
--- /dev/null
+++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb
@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'Abseil'
+version = '20230125.3'
+
+homepage = 'https://abseil.io/'
+description = """Abseil is an open-source collection of C++ library code designed to augment the
+C++ standard library. The Abseil library code is collected from Google's own
+C++ code base, has been extensively tested and used in production, and is the
+same code we depend on in our daily coding lives."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True, 'cstd': 'c++17'}
+
+source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags']
+sources = ['%(version)s.tar.gz']
+checksums = ['5366d7e7fa7ba0d915014d387b66d0d002c03236448e1ba9ef98122c13b35c36']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+
+sanity_check_paths = {
+    'files': ['lib/libabsl_base.%s' % SHLIB_EXT],
+    'dirs': ['include/absl'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..eb9097baf3e
--- /dev/null
+++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'CMakeMake'
+
+name = 'Blitz++'
+version = '1.0.2'
+
+homepage = 'https://github.com/blitzpp/blitz'
+
+description = """
+ Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation
+ in C++ with a speed comparable to Fortran implementations, while preserving an
+ object-oriented interface
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [('https://github.com/blitzpp/blitz/archive/')]
+sources = ['%(version)s.tar.gz']
+patches = ['blitz-%(version)s_pkgconfig.patch']
+checksums = [
+    {'1.0.2.tar.gz': '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'},
+    {'blitz-1.0.2_pkgconfig.patch': 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3')
+]
+
+sanity_check_paths = {
+    'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT],
+    'dirs': ['include/blitz/array', 'include/blitz/meta',
+             'include/random', 'lib64/pkgconfig'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..957f3fbd53c
--- /dev/null
+++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb
@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'groff'
+version = '1.22.4'
+
+homepage = 'https://www.gnu.org/software/groff'
+description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands
+ and produces formatted output."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://ftp.gnu.org/gnu/groff']
+sources = [SOURCE_TAR_GZ]
+checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+configopts = '--with-doc=no'
+
+sanity_check_paths = {
+    'files': ['bin/groff', 'bin/nroff', 'bin/troff'],
+    'dirs': ['lib/groff', 'share'],
+}
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..50a777efb87
--- /dev/null
+++ b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'json-c'
+version = '0.16'
+local_suff = '-20220414'
+
+homepage = 'https://github.com/json-c/json-c'
+description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects
+ in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON
+objects."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/json-c/json-c/archive/']
+sources = ['json-c-%%(version)s%s.tar.gz' % local_suff]
+checksums = ['3ecaeedffd99a60b1262819f9e60d7d983844073abc74e495cb822b251904185']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind
+pretestopts = 'USE_VALGRIND=0 '
+runtest = 'test'
+
+sanity_check_paths = {
+    'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'],
+    'dirs': ['include/json-c'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..f11da8ce849
--- /dev/null
+++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'libgeotiff'
+version = '1.7.1'
+
+homepage = 'https://directory.fsf.org/wiki/Libgeotiff'
+description = """Library for reading and writing coordinate system information from/to GeoTIFF files"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://download.osgeo.org/geotiff/libgeotiff']
+sources = [SOURCE_TAR_GZ]
+checksums = ['05ab1347aaa471fc97347d8d4269ff0c00f30fa666d956baba37948ec87e55d6']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('PROJ', '9.2.0'),
+    ('libjpeg-turbo', '2.1.5.1'),
+    ('zlib', '1.2.13'),
+    ('SQLite', '3.42.0'),
+    ('LibTIFF', '4.5.0'),
+    ('cURL', '8.0.1'),
+]
+
+configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB'
+configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO'
+
+sanity_check_paths = {
+    'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..409cc8bc2a0
--- /dev/null
+++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'libtirpc'
+version = '1.3.3'
+
+homepage = 'https://sourceforge.net/projects/libtirpc/'
+description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCE_TAR_BZ2]
+checksums = ['6474e98851d9f6f33871957ddee9714fdcd9d8a5ee9abb5a98d63ea2e60e12f3']
+
+configopts = '--enable-static --enable-shared --disable-gssapi'
+
+builddependencies = [
+    ('binutils', '2.40')
+]
+
+sanity_check_paths = {
+    'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]],
+    'dirs': ['include/tirpc', 'lib'],
+}
+
+modextrapaths = {'CPATH': 'include/tirpc'}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..171353e0fac
--- /dev/null
+++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'ConfigureMake'
+
+name = 'libxslt'
+version = '1.1.38'
+
+homepage = 'http://xmlsoft.org/'
+description = """Libxslt is the XSLT C library developed for the GNOME project
+ (but usable outside of the Gnome platform)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['1f32450425819a09acaff2ab7a5a7f8a2ec7956e505d7beeb45e843d0e1ecab1']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('pkgconf', '1.9.5'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('libxml2', '2.11.4'),
+]
+
+# Make sure it doesn't pick up OS installed libgcrypt or Python
+configopts = '--with-crypto=no --with-python=no '
+
+sanity_check_paths = {
+    'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..76fee75bd36
--- /dev/null
+++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'libyaml'
+version = '0.2.5'
+
+homepage = 'https://pyyaml.org/wiki/LibYAML'
+description = "LibYAML is a YAML parser and emitter written in C."
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://pyyaml.org/download/%(name)s/']
+sources = ['yaml-%(version)s.tar.gz']
+checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+
+sanity_check_paths = {
+    'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..2a363ae76ca
--- /dev/null
+++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb
@@ -0,0 +1,36 @@
+name = 'METIS'
+version = '5.1.0'
+
+homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
+
+description = """
+ METIS is a set of serial programs for partitioning graphs, partitioning
+ finite element meshes, and producing fill reducing orderings for sparse
+ matrices. The algorithms implemented in METIS are based on the multilevel
+ recursive-bisection, multilevel k-way, and multi-constraint partitioning
+ schemes.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = [
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis',
+    'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s-use-doubles.patch']
+checksums = [
+    {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'},
+    {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'},
+]
+
+# We use 32bit for indices and 64bit for content
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+configopts = ['', 'shared=1']
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..1ad7b6c1af6
--- /dev/null
+++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb
@@ -0,0 +1,25 @@
+easyblock = 'CMakeMake'
+
+name = 'nlohmann_json'
+version = '3.11.2'
+
+homepage = 'https://github.com/nlohmann/json'
+description = """JSON for Modern C++"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['d69f9deb6a75e2580465c6c4c5111b89c4dc2fa94e3a85fcd2ffcd9a143d9273']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+sanity_check_paths = {
+    'files': ['include/nlohmann/json.hpp'],
+    'dirs': ['share/cmake', 'share/pkgconfig'],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..deb26d4ed5d
--- /dev/null
+++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb
@@ -0,0 +1,49 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2014-2015 The Cyprus Institute
+# Authors:: Thekla Loizou <t.loizou@cyi.ac.cy>
+# License:: MIT/GPL
+#
+##
+easyblock = 'CMakeMake'
+
+name = 'PROJ'
+version = '9.2.0'
+
+homepage = 'https://proj.org'
+description = """Program proj is a standard Unix filter function which converts
+geographic longitude and latitude coordinates into cartesian coordinates"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://download.osgeo.org/proj/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['dea816f5aa732ae6b2ee3977b9bdb28b1d848cf56a1aad8faf6708b89f0ed50e']
+
+builddependencies = [
+    ('pkgconf', '1.9.5'),
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('googletest', '1.13.0'),
+]
+
+dependencies = [
+    ('SQLite', '3.42.0'),
+    ('LibTIFF', '4.5.0'),
+    ('cURL', '8.0.1'),
+    ('XZ', '5.4.2'),
+    ('nlohmann_json', '3.11.2'),
+]
+
+# build twice, once for static, once for shared libraries
+configopts = ['', '-DBUILD_SHARED_LIBS=OFF']
+
+sanity_check_paths = {
+    'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo',
+              'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'

From 62162245805637fc813294cdcc38fd4a933a3935 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 22 May 2023 11:03:37 +0200
Subject: [PATCH 587/601] adding easyconfigs: ripunzip-0.4.0.eb

---
 .../easyconfigs/r/ripunzip/ripunzip-0.4.0.eb  | 484 ++++++++++++++++++
 1 file changed, 484 insertions(+)
 create mode 100644 easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb

diff --git a/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb b/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb
new file mode 100644
index 00000000000..ef9b2d15dd9
--- /dev/null
+++ b/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb
@@ -0,0 +1,484 @@
+easyblock = 'Cargo'
+
+name = 'ripunzip'
+version = '0.4.0'
+
+homepage = 'https://github.com/google/ripunzip'
+description = "A tool to unzip files in parallel."
+
+toolchain = SYSTEM
+
+crates = [
+    ('adler', '1.0.2'),
+    ('aes', '0.7.5'),
+    ('aho-corasick', '0.7.20'),
+    ('anyhow', '1.0.66'),
+    ('arbitrary', '1.2.0'),
+    ('arrayvec', '0.5.2'),
+    ('atty', '0.2.14'),
+    ('autocfg', '1.1.0'),
+    ('base64', '0.13.1'),
+    ('base64ct', '1.5.3'),
+    ('bitflags', '1.3.2'),
+    ('block-buffer', '0.10.3'),
+    ('bstr', '0.2.17'),
+    ('bumpalo', '3.11.1'),
+    ('byteorder', '1.4.3'),
+    ('bytes', '1.3.0'),
+    ('bzip2', '0.4.3'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cast', '0.3.0'),
+    ('cc', '1.0.77'),
+    ('cfg-if', '1.0.0'),
+    ('cipher', '0.3.0'),
+    ('clap', '2.34.0'),
+    ('clap', '4.0.29'),
+    ('clap_derive', '4.0.21'),
+    ('clap_lex', '0.3.0'),
+    ('console', '0.15.2'),
+    ('constant_time_eq', '0.1.5'),
+    ('core-foundation', '0.9.3'),
+    ('core-foundation-sys', '0.8.3'),
+    ('cpufeatures', '0.2.5'),
+    ('crc32fast', '1.3.2'),
+    ('criterion', '0.3.6'),
+    ('criterion-plot', '0.4.5'),
+    ('crossbeam-channel', '0.5.6'),
+    ('crossbeam-deque', '0.8.2'),
+    ('crossbeam-epoch', '0.9.13'),
+    ('crossbeam-utils', '0.8.14'),
+    ('crypto-common', '0.1.6'),
+    ('csv', '1.1.6'),
+    ('csv-core', '0.1.10'),
+    ('derive_arbitrary', '1.2.1'),
+    ('digest', '0.10.6'),
+    ('either', '1.8.0'),
+    ('encode_unicode', '0.3.6'),
+    ('encoding_rs', '0.8.31'),
+    ('env_logger', '0.10.0'),
+    ('errno', '0.2.8'),
+    ('errno-dragonfly', '0.1.2'),
+    ('fastrand', '1.8.0'),
+    ('flate2', '1.0.25'),
+    ('fnv', '1.0.7'),
+    ('foreign-types', '0.3.2'),
+    ('foreign-types-shared', '0.1.1'),
+    ('form_urlencoded', '1.1.0'),
+    ('futures', '0.3.25'),
+    ('futures-channel', '0.3.25'),
+    ('futures-core', '0.3.25'),
+    ('futures-io', '0.3.25'),
+    ('futures-macro', '0.3.25'),
+    ('futures-sink', '0.3.25'),
+    ('futures-task', '0.3.25'),
+    ('futures-util', '0.3.25'),
+    ('generic-array', '0.14.6'),
+    ('getrandom', '0.2.8'),
+    ('h2', '0.3.15'),
+    ('half', '1.8.2'),
+    ('hashbrown', '0.12.3'),
+    ('heck', '0.4.0'),
+    ('hermit-abi', '0.1.19'),
+    ('hermit-abi', '0.2.6'),
+    ('hexdump', '0.1.1'),
+    ('hmac', '0.12.1'),
+    ('http', '0.2.8'),
+    ('http-body', '0.4.5'),
+    ('httparse', '1.8.0'),
+    ('httpdate', '1.0.2'),
+    ('httptest', '0.15.4'),
+    ('humantime', '2.1.0'),
+    ('hyper', '0.14.23'),
+    ('hyper-tls', '0.5.0'),
+    ('idna', '0.3.0'),
+    ('indexmap', '1.9.2'),
+    ('indicatif', '0.17.2'),
+    ('instant', '0.1.12'),
+    ('io-lifetimes', '1.0.3'),
+    ('ipnet', '2.5.1'),
+    ('is-terminal', '0.4.1'),
+    ('itertools', '0.4.19'),
+    ('itertools', '0.10.5'),
+    ('itoa', '0.4.8'),
+    ('itoa', '1.0.4'),
+    ('jobserver', '0.1.25'),
+    ('js-sys', '0.3.60'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.138'),
+    ('linux-raw-sys', '0.1.3'),
+    ('lipsum', '0.8.2'),
+    ('log', '0.4.17'),
+    ('memchr', '2.5.0'),
+    ('memoffset', '0.7.1'),
+    ('mime', '0.3.16'),
+    ('miniz_oxide', '0.6.2'),
+    ('mio', '0.8.5'),
+    ('monitor', '0.1.0'),
+    ('native-tls', '0.2.11'),
+    ('num-traits', '0.2.15'),
+    ('num_cpus', '1.14.0'),
+    ('number_prefix', '0.4.0'),
+    ('once_cell', '1.16.0'),
+    ('oorandom', '11.1.3'),
+    ('opaque-debug', '0.3.0'),
+    ('openssl', '0.10.44'),
+    ('openssl-macros', '0.1.0'),
+    ('openssl-probe', '0.1.5'),
+    ('openssl-sys', '0.9.79'),
+    ('os_str_bytes', '6.4.1'),
+    ('password-hash', '0.4.2'),
+    ('pbkdf2', '0.11.0'),
+    ('percent-encoding', '2.2.0'),
+    ('pin-project-lite', '0.2.9'),
+    ('pin-utils', '0.1.0'),
+    ('pkg-config', '0.3.26'),
+    ('plotters', '0.3.4'),
+    ('plotters-backend', '0.3.4'),
+    ('plotters-svg', '0.3.3'),
+    ('portable-atomic', '0.3.15'),
+    ('ppv-lite86', '0.2.17'),
+    ('proc-macro-error', '1.0.4'),
+    ('proc-macro-error-attr', '1.0.4'),
+    ('proc-macro2', '1.0.47'),
+    ('progress-streams', '1.1.0'),
+    ('quote', '1.0.21'),
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+    {'termcolor-1.1.3.tar.gz': 'bab24d30b911b2376f3a13cc2cd443142f0c81dda04c118693e35b3835757755'},
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+    {'tokio-util-0.7.4.tar.gz': '0bb2e075f03b3d66d8d8785356224ba688d2906a371015e225beeb65ca92c740'},
+    {'tower-service-0.3.2.tar.gz': 'b6bc1c9ce2b5135ac7f93c72918fc37feb872bdc6a5533a8b85eb4b86bfdae52'},
+    {'tracing-0.1.37.tar.gz': '8ce8c33a8d48bd45d624a6e523445fd21ec13d3653cd51f681abf67418f54eb8'},
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+    {'try-lock-0.2.3.tar.gz': '59547bce71d9c38b83d9c0e92b6066c4253371f15005def0c30d9657f50c7642'},
+    {'typenum-1.16.0.tar.gz': '497961ef93d974e23eb6f433eb5fe1b7930b659f06d12dec6fc44a8f554c0bba'},
+    {'unicode-bidi-0.3.8.tar.gz': '099b7128301d285f79ddd55b9a83d5e6b9e97c92e0ea0daebee7263e932de992'},
+    {'unicode-ident-1.0.5.tar.gz': '6ceab39d59e4c9499d4e5a8ee0e2735b891bb7308ac83dfb4e80cad195c9f6f3'},
+    {'unicode-normalization-0.1.22.tar.gz': '5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921'},
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+    {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'},
+    {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'},
+    {'walkdir-2.3.2.tar.gz': '808cf2735cd4b6866113f648b791c6adc5714537bc222d9347bb203386ffda56'},
+    {'want-0.3.0.tar.gz': '1ce8a968cb1cd110d136ff8b819a556d6fb6d919363c61534f6860c7eb172ba0'},
+    {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'},
+    {'wasm-bindgen-0.2.83.tar.gz': 'eaf9f5aceeec8be17c128b2e93e031fb8a4d469bb9c4ae2d7dc1888b26887268'},
+    {'wasm-bindgen-backend-0.2.83.tar.gz': '4c8ffb332579b0557b52d268b91feab8df3615f265d5270fec2a8c95b17c1142'},
+    {'wasm-bindgen-futures-0.4.33.tar.gz': '23639446165ca5a5de86ae1d8896b737ae80319560fbaa4c2887b7da6e7ebd7d'},
+    {'wasm-bindgen-macro-0.2.83.tar.gz': '052be0f94026e6cbc75cdefc9bae13fd6052cdcaf532fa6c45e7ae33a1e6c810'},
+    {'wasm-bindgen-macro-support-0.2.83.tar.gz': '07bc0c051dc5f23e307b13285f9d75df86bfdf816c5721e573dec1f9b8aa193c'},
+    {'wasm-bindgen-shared-0.2.83.tar.gz': '1c38c045535d93ec4f0b4defec448e4291638ee608530863b1e2ba115d4fff7f'},
+    {'web-sys-0.3.60.tar.gz': 'bcda906d8be16e728fd5adc5b729afad4e444e106ab28cd1c7256e54fa61510f'},
+    {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'},
+    {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'},
+    {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'},
+    {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'},
+    {'windows-sys-0.36.1.tar.gz': 'ea04155a16a59f9eab786fe12a4a450e75cdb175f9e0d80da1e17db09f55b8d2'},
+    {'windows-sys-0.42.0.tar.gz': '5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7'},
+    {'windows_aarch64_gnullvm-0.42.0.tar.gz': '41d2aa71f6f0cbe00ae5167d90ef3cfe66527d6f613ca78ac8024c3ccab9a19e'},
+    {'windows_aarch64_msvc-0.36.1.tar.gz': '9bb8c3fd39ade2d67e9874ac4f3db21f0d710bee00fe7cab16949ec184eeaa47'},
+    {'windows_aarch64_msvc-0.42.0.tar.gz': 'dd0f252f5a35cac83d6311b2e795981f5ee6e67eb1f9a7f64eb4500fbc4dcdb4'},
+    {'windows_i686_gnu-0.36.1.tar.gz': '180e6ccf01daf4c426b846dfc66db1fc518f074baa793aa7d9b9aaeffad6a3b6'},
+    {'windows_i686_gnu-0.42.0.tar.gz': 'fbeae19f6716841636c28d695375df17562ca208b2b7d0dc47635a50ae6c5de7'},
+    {'windows_i686_msvc-0.36.1.tar.gz': 'e2e7917148b2812d1eeafaeb22a97e4813dfa60a3f8f78ebe204bcc88f12f024'},
+    {'windows_i686_msvc-0.42.0.tar.gz': '84c12f65daa39dd2babe6e442988fc329d6243fdce47d7d2d155b8d874862246'},
+    {'windows_x86_64_gnu-0.36.1.tar.gz': '4dcd171b8776c41b97521e5da127a2d86ad280114807d0b2ab1e462bc764d9e1'},
+    {'windows_x86_64_gnu-0.42.0.tar.gz': 'bf7b1b21b5362cbc318f686150e5bcea75ecedc74dd157d874d754a2ca44b0ed'},
+    {'windows_x86_64_gnullvm-0.42.0.tar.gz': '09d525d2ba30eeb3297665bd434a54297e4170c7f1a44cad4ef58095b4cd2028'},
+    {'windows_x86_64_msvc-0.36.1.tar.gz': 'c811ca4a8c853ef420abd8592ba53ddbbac90410fab6903b3e79972a631f7680'},
+    {'windows_x86_64_msvc-0.42.0.tar.gz': 'f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5'},
+    {'winreg-0.10.1.tar.gz': '80d0f4e272c85def139476380b12f9ac60926689dd2e01d4923222f40580869d'},
+    {'zip-0.6.3.tar.gz': '537ce7411d25e54e8ae21a7ce0b15840e7bfcff15b51d697ec3266cc76bdf080'},
+    {'zstd-0.11.2+zstd.1.5.2.tar.gz': '20cc960326ece64f010d2d2107537f26dc589a6573a316bd5b1dba685fa5fde4'},
+    {'zstd-safe-5.0.2+zstd.1.5.2.tar.gz': '1d2a5585e04f9eea4b2a3d1eca508c4dee9592a89ef6f450c11719da0726f4db'},
+    {'zstd-sys-2.0.4+zstd.1.5.2.tar.gz': '4fa202f2ef00074143e219d15b62ffc317d17cc33909feac471c044087cad7b0'},
+]
+
+builddependencies = [
+    ('Rust', '1.65.0', '', ('GCCcore', '12.2.0')),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ripunzip'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["ripunzip --help"]
+
+moduleclass = 'tools'

From a70763dd99846e9ba31ebb5ba6c962db1f9a4d0a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 22 May 2023 14:10:58 +0200
Subject: [PATCH 588/601] fix dependency of Braindecode v0.7 on PyTorch

---
 ...=> Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb} | 2 +-
 ...h-1.10.2.eb => Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb} | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)
 rename easybuild/easyconfigs/b/Braindecode/{Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb => Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb} (94%)
 rename easybuild/easyconfigs/b/Braindecode/{Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb => Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb} (96%)

diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb
similarity index 94%
rename from easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb
rename to easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb
index 6e6c6ca13e1..10e39d0b33e 100644
--- a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb
@@ -2,7 +2,7 @@ easyblock = 'PythonBundle'
 
 name = 'Braindecode'
 version = '0.7'
-versionsuffix = '-PyTorch-1.10.2-CUDA-%(cudaver)s'
+versionsuffix = '-PyTorch-1.10.0-CUDA-%(cudaver)s'
 
 homepage = 'https://braindecode.org/'
 description = """Braindecode is an open-source Python toolbox for decoding raw
diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb
similarity index 96%
rename from easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb
rename to easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb
index c503d33df9c..9780e1b0bc1 100644
--- a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb
+++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb
@@ -2,7 +2,7 @@ easyblock = 'PythonBundle'
 
 name = 'Braindecode'
 version = '0.7'
-versionsuffix = '-PyTorch-1.10.2'
+versionsuffix = '-PyTorch-1.10.0'
 
 homepage = 'https://braindecode.org/'
 description = """Braindecode is an open-source Python toolbox for decoding raw

From f8e14f9ba0fae82f216cbd8860238ad496414dda Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 22 May 2023 14:11:21 +0200
Subject: [PATCH 589/601] adding easyconfigs: MOABB-0.4.6-foss-2021a.eb

---
 .../m/MOABB/MOABB-0.4.6-foss-2021a.eb         | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb

diff --git a/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb b/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb
new file mode 100644
index 00000000000..dffd885177d
--- /dev/null
+++ b/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'MOABB'
+version = '0.4.6'
+
+homepage = 'https://neurotechx.github.io/moabb/'
+description = """Build a comprehensive benchmark of popular Brain-Computer Interface (BCI)
+algorithms applied on an extensive list of freely available EEG datasets."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('MNE-Python', '0.24.1'),
+    ('h5py', '3.2.1'),
+    ('scikit-learn', '0.24.2'),
+    ('matplotlib', '3.4.2'),
+    ('Seaborn', '0.11.2'),
+    ('PyYAML', '5.4.1'),
+    ('tqdm', '4.61.2'),
+]
+
+use_pip = True
+
+# relax requirements of unmatchable dependencies (requirements seem quite arbitrary)
+_relax_req = ';'.join(['s/^%s.*/%s = "*"/' % (d, d) for d in ['scikit-learn', 'tqdm']])
+
+exts_list = [
+    ('pooch', '1.6.0', {
+        'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'],
+    }),
+    ('coverage', '5.5', {
+        'checksums': ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'],
+    }),
+    ('pyriemann', '0.2.7', {
+        'checksums': ['1feed8f72d94414bdc9ca4485333711a3f91f9742ae8794874a7399f4166758a'],
+    }),
+    ('moabb', version, {
+        'preinstallopts': "sed -i '%s' pyproject.toml &&" % _relax_req,
+        'checksums': ['4278be10aa721ba3ced0b03037901cccfeaeca6d04f7a157f1cf42f60395757d'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'tools'

From 8357b48c2f784b23a7b4d414c648d78ec83f5edf Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 22 May 2023 14:21:10 +0200
Subject: [PATCH 590/601] add exisiting author contributions to mstore

---
 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
index 8ddbf0c4fc0..a8015f4cc5f 100644
--- a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb
@@ -1,3 +1,5 @@
+# J. Sassmannshausen (Imperial College London/UK)
+
 easyblock = 'CMakeMake'
 
 name = 'mstore'

From a44e30ce8513cf5ff02978fb426c5f970c16ac73 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 22 May 2023 14:22:48 +0200
Subject: [PATCH 591/601] explain runtest command in
 Simple-DFTD3-0.7.0-foss-2022a.eb

---
 .../easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
index 4d92d2d0cde..f2575df8691 100644
--- a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
+++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb
@@ -34,6 +34,7 @@ build_shared_libs = True
 
 configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1'
 
+# run suite of tests with ctest
 test_cmd = 'ctest'
 runtest = ''
 

From 845b7e951a8011a7d8950b42173869275dc6a639 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 22 May 2023 14:58:46 +0200
Subject: [PATCH 592/601] adding easyconfigs:
 skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb

---
 ...0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb

diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb
new file mode 100644
index 00000000000..6e5bfbf74c3
--- /dev/null
+++ b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb
@@ -0,0 +1,29 @@
+easyblock = 'PythonPackage'
+
+name = 'skorch'
+version = '0.11.0'
+local_pt_version = '1.10.0'
+versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pt_version
+
+homepage = 'https://skorch.readthedocs.io/'
+description = "A scikit-learn compatible neural network library that wraps PyTorch."
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['b35cb4e50045742f0ffcfad33044af691d5d36b50212573753a804483a947ca9']
+
+dependencies = [
+    ('CUDA', '11.3.1', '', SYSTEM),
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('scikit-learn', '0.24.2'),
+    ('tqdm', '4.61.2'),
+    ('PyTorch', local_pt_version, '-CUDA-%(cudaver)s'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'data'

From cff99850291fdbe4acb114364b3835209dbffe72 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Mon, 15 May 2023 17:25:26 +0200
Subject: [PATCH 593/601] fix test_quantization in PyTorch 1.12.1

---
 .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb  |  3 +++
 .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb    |  3 +++
 .../PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb  |  3 +++
 .../p/PyTorch/PyTorch-1.12.1-foss-2021b.eb    |  3 +++
 .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb  |  3 +++
 .../p/PyTorch/PyTorch-1.12.1-foss-2022a.eb    |  3 +++
 ...ch-1.12.1_add-hypothesis-suppression.patch | 20 +++++++++++++++++++
 7 files changed, 38 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
index df2f07b6db3..855d6a9bfdd 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb
@@ -25,6 +25,7 @@ patches = [
     'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
     'PyTorch-1.11.0_install-vsx-vec-headers.patch',
     'PyTorch-1.11.1_skip-test_init_from_local_shards.patch',
+    'PyTorch-1.12.1_add-hypothesis-suppression.patch',
     'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
     'PyTorch-1.12.1_fix-skip-decorators.patch',
     'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
@@ -63,6 +64,8 @@ checksums = [
     'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
     # PyTorch-1.11.1_skip-test_init_from_local_shards.patch
     '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7',
+    # PyTorch-1.12.1_add-hypothesis-suppression.patch
+    'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c',
     # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
     'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab',
     'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c',  # PyTorch-1.12.1_fix-skip-decorators.patch
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
index 550c24d748b..b8fd4fe4a0b 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb
@@ -23,6 +23,7 @@ patches = [
     'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch',
     'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
     'PyTorch-1.11.0_install-vsx-vec-headers.patch',
+    'PyTorch-1.12.1_add-hypothesis-suppression.patch',
     'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
     'PyTorch-1.12.1_fix-skip-decorators.patch',
     'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
@@ -59,6 +60,8 @@ checksums = [
     # PyTorch-1.11.0_increase-distributed-test-timeout.patch
     '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f',
     'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
+    # PyTorch-1.12.1_add-hypothesis-suppression.patch
+    'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c',
     # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
     'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab',
     'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c',  # PyTorch-1.12.1_fix-skip-decorators.patch
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
index 3ce09263594..b8bf2014778 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb
@@ -25,6 +25,7 @@ patches = [
     'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
     'PyTorch-1.11.0_install-vsx-vec-headers.patch',
     'PyTorch-1.11.1_skip-test_init_from_local_shards.patch',
+    'PyTorch-1.12.1_add-hypothesis-suppression.patch',
     'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch',
     'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
     'PyTorch-1.12.1_fix-skip-decorators.patch',
@@ -68,6 +69,8 @@ checksums = [
     'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
     # PyTorch-1.11.1_skip-test_init_from_local_shards.patch
     '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7',
+    # PyTorch-1.12.1_add-hypothesis-suppression.patch
+    'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c',
     # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch
     'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089',
     # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
index b4ca5e1483a..a6e1886d545 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb
@@ -23,6 +23,7 @@ patches = [
     'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch',
     'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
     'PyTorch-1.11.0_install-vsx-vec-headers.patch',
+    'PyTorch-1.12.1_add-hypothesis-suppression.patch',
     'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
     'PyTorch-1.12.1_fix-skip-decorators.patch',
     'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
@@ -63,6 +64,8 @@ checksums = [
     # PyTorch-1.11.0_increase-distributed-test-timeout.patch
     '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f',
     'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
+    # PyTorch-1.12.1_add-hypothesis-suppression.patch
+    'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c',
     # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
     'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab',
     'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c',  # PyTorch-1.12.1_fix-skip-decorators.patch
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
index 8cc442f469d..f7cf757ee24 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb
@@ -25,6 +25,7 @@ patches = [
     'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
     'PyTorch-1.11.0_install-vsx-vec-headers.patch',
     'PyTorch-1.11.1_skip-test_init_from_local_shards.patch',
+    'PyTorch-1.12.1_add-hypothesis-suppression.patch',
     'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch',
     'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
     'PyTorch-1.12.1_fix-skip-decorators.patch',
@@ -68,6 +69,8 @@ checksums = [
     'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
     # PyTorch-1.11.1_skip-test_init_from_local_shards.patch
     '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7',
+    # PyTorch-1.12.1_add-hypothesis-suppression.patch
+    'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c',
     # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch
     'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089',
     # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
index 3f02df492ba..2d70b6c97a8 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb
@@ -23,6 +23,7 @@ patches = [
     'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch',
     'PyTorch-1.11.0_increase-distributed-test-timeout.patch',
     'PyTorch-1.11.0_install-vsx-vec-headers.patch',
+    'PyTorch-1.12.1_add-hypothesis-suppression.patch',
     'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch',
     'PyTorch-1.12.1_fix-skip-decorators.patch',
     'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
@@ -63,6 +64,8 @@ checksums = [
     # PyTorch-1.11.0_increase-distributed-test-timeout.patch
     '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f',
     'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d',  # PyTorch-1.11.0_install-vsx-vec-headers.patch
+    # PyTorch-1.12.1_add-hypothesis-suppression.patch
+    'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c',
     # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch
     'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab',
     'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c',  # PyTorch-1.12.1_fix-skip-decorators.patch
diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch
new file mode 100644
index 00000000000..43a08b24044
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch
@@ -0,0 +1,20 @@
+The @settings decorator overwrites `suppress_health_check` accidentally removing the `too_slow` filter
+inherited by the profile.
+Add it explicitely.
+See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615#issuecomment-1504930435
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/test/quantization/core/test_quantized_op.py b/test/quantization/core/test_quantized_op.py
+index 41e90bc6ec7..c19324cf86a 100644
+--- a/test/quantization/core/test_quantized_op.py
++++ b/test/quantization/core/test_quantized_op.py
+@@ -5569,7 +5569,7 @@ class TestQNNPackOps(TestCase):
+                              msg="QNNPACK Sigmoid failed (FBGEMM ref)!")
+ 
+     """Tests the correctness of the quantized::add (qnnpack) op."""
+-    @settings(suppress_health_check=(HealthCheck.filter_too_much,))
++    @settings(suppress_health_check=(HealthCheck.filter_too_much, HealthCheck.too_slow))
+     @given(A=hu.tensor(shapes=hu.array_shapes(1, 5, 1, 5),
+                        qparams=hu.qparams(dtypes=[torch.quint8, torch.qint8])),
+            zero_point=st.sampled_from([0, 2, 5, 15, 127]),

From d24faf90b2afe419f74ad7f16b5e2be67dea9bfb Mon Sep 17 00:00:00 2001
From: Balazs Hajgato <Balazs.Hajgato@UGent.be>
Date: Tue, 23 May 2023 15:42:47 +0200
Subject: [PATCH 594/601] {chem}[gomkl/2021a] ASE 3.22.1

---
 .../a/ASE/ASE-3.22.1-gomkl-2021a.eb           | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb

diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb
new file mode 100644
index 00000000000..cefd29a8957
--- /dev/null
+++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb
@@ -0,0 +1,47 @@
+easyblock = 'PythonBundle'
+
+name = 'ASE'
+version = '3.22.1'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language.
+
+From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations
+in C of functions in ASE.  ASE uses it automatically when installed."""
+
+toolchain = {'name': 'gomkl', 'version': '2021a'}
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('SciPy-bundle', '2021.05'),
+    ('Flask', '1.1.4'),
+    ('matplotlib', '3.4.2'),
+    ('Tkinter', '%(pyver)s'),     # Needed by GUI of ASE
+    ('spglib-python', '1.16.1'),  # optional
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('pytest-mock', '3.6.1', {
+        'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'],
+    }),
+    ('ase', version, {
+        'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'],
+    }),
+    ('ase-ext', '20.9.0', {
+        'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+# make sure Tkinter is available, otherwise 'ase gui' will not work
+sanity_check_commands = ["python -c 'import tkinter' "]
+
+moduleclass = 'chem'

From 9790218cd6faed35a4d03d754db7d44da8c0f66a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 May 2023 18:29:16 +0200
Subject: [PATCH 595/601] adding easyconfigs: awscli-2.11.21-GCCcore-11.3.0.eb

---
 .../a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb | 62 +++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb
new file mode 100644
index 00000000000..080aebf9855
--- /dev/null
+++ b/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb
@@ -0,0 +1,62 @@
+easyblock = 'PythonBundle'
+
+name = 'awscli'
+version = '2.11.21'
+
+homepage = 'https://pypi.python.org/pypi/awscli'
+description = 'Universal Command Line Environment for AWS'
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [
+    ('binutils', '2.38'),
+    ('CMake', '3.24.3'),  # required for awscrt
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('PyYAML', '6.0'),
+    ('ruamel.yaml', '0.17.21'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('jmespath', '1.0.1', {
+        'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'],
+    }),
+    ('botocore', '1.29.138', {
+        'checksums': ['31edc237088c104f7a05887646bbec31d7459dd2e108fd90cbffa315902817e2'],
+    }),
+    ('s3transfer', '0.6.1', {
+        'checksums': ['640bb492711f4c0c0905e1f62b6aaeb771881935ad27884852411f8e9cacbca9'],
+    }),
+    ('prompt-toolkit', '3.0.38', {
+        'sources': ['prompt_toolkit-%(version)s.tar.gz'],
+        'checksums': ['23ac5d50538a9a38c8bde05fecb47d0b403ecd0662857a86f886f798563d5b9b'],
+    }),
+    ('distro', '1.8.0', {
+        'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'],
+    }),
+    ('awscrt', '0.16.16', {
+        'checksums': ['13075df2c1d7942fe22327b6483274517ee0f6ae765c4e6b6ae9ef5b4c43a827'],
+        # cfr. https://github.com/awslabs/aws-crt-python/tree/main#openssl-and-libcrypto-unix-only
+        'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ",
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/aws/aws-cli/archive/'],
+        'source_tmpl': '%(version)s.tar.gz',
+        'checksums': ['74b6f7b1d773eafdefbb0972ea8db68be6814d382d7406707e94a25a0e6c1ebf'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/aws'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/'],
+}
+
+sanity_check_commands = ["aws help"]
+
+moduleclass = 'tools'

From 1d9d14e9abfb39fa653b8aac8e285fb13f3718d4 Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Wed, 24 May 2023 09:31:19 +0100
Subject: [PATCH 596/601] adding easyconfigs:
 pytest-cpp-2.3.0-GCCcore-11.3.0.eb,
 pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb

---
 .../pytest-cpp-2.3.0-GCCcore-11.3.0.eb        | 21 +++++++++++++++++++
 ...pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb | 21 +++++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100755 easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb
 create mode 100755 easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb
new file mode 100755
index 00000000000..f5d720e5b7a
--- /dev/null
+++ b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb
@@ -0,0 +1,21 @@
+easyblock = 'PythonPackage'
+
+name = 'pytest-cpp'
+version = '2.3.0'
+
+homepage = 'http://github.com/pytest-dev/pytest-cpp'
+description = """Use pytest runner to discover and execute C++ tests."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+dependencies = [('Python', '3.10.4')]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = False
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['37abfa693697940aed2e7c034698188dee3616183ad9b3f764f3b06aeb75ed4a']
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb
new file mode 100755
index 00000000000..af5753f1645
--- /dev/null
+++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb
@@ -0,0 +1,21 @@
+easyblock = 'PythonPackage'
+
+name = 'pytest-flakefinder'
+version = '1.1.0'
+
+homepage = 'https://github.com/dropbox/pytest-flakefinder'
+description = """Runs tests multiple times to expose flakiness."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+dependencies = [('Python', '3.10.4')]
+
+use_pip = True
+sanity_pip_check = True
+download_dep_fail = False
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e']
+
+moduleclass = 'tools'

From bbe7cdff7b5266c36303b17cab854110eaf97c33 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 May 2023 13:25:00 +0200
Subject: [PATCH 597/601] fix download of R-transport by adding archive source
 URL

---
 .../r/R-transport/R-transport-0.13-0-foss-2021b.eb           | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb
index a025135e559..fbc8b3c32f9 100644
--- a/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb
+++ b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb
@@ -9,7 +9,10 @@ description = "transport: Computation of Optimal Transport Plans and Wasserstein
 
 toolchain = {'name': 'foss', 'version': '2021b'}
 
-source_urls = ['https://cran.r-project.org/src/contrib/']
+source_urls = [
+    'https://cran.r-project.org/src/contrib/Archive/transport/',
+    'https://cran.r-project.org/src/contrib/',
+]
 sources = ['%s_%%(version)s.tar.gz' % local_rpkg]
 checksums = ['c55efbdd93e36e92ef39e4b9529ee64c3c7ecb965d77ec9c469a7c56c93f5f57']
 

From 2878c4273d73b9c6ce0702ea3c0593b68c8473f5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 May 2023 17:51:21 +0200
Subject: [PATCH 598/601] add binutils build dependency in Evcxr-REPL
 easyconfig

---
 .../Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb           | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb
index b3535b944b2..90325d9c67c 100644
--- a/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb
+++ b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb
@@ -442,6 +442,10 @@ checksums = [
     {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'},
 ]
 
+builddependencies = [
+    ('binutils', '2.39'),
+]
+
 dependencies = [
     ('Rust', local_rustver),
 ]

From 7bfaeaa8d48294bfc98cbf4245329ca50b80b9fc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 May 2023 18:06:58 +0200
Subject: [PATCH 599/601] don't require custom sanity_check_paths when using
 CargoPythonPackage, since it inherits a decent sanity_check_paths from
 PythonPackage

---
 test/easyconfigs/easyconfigs.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py
index 40c597ba675..4e9b5508fd7 100644
--- a/test/easyconfigs/easyconfigs.py
+++ b/test/easyconfigs/easyconfigs.py
@@ -1124,10 +1124,10 @@ def test_pr_sanity_check_paths(self):
         """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock."""
 
         # some generic easyblocks already have a decent customised sanity_check_paths,
-        # including CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage;
+        # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage;
         # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check.
-        whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC',
-                     'PythonBundle', 'PythonPackage', 'Toolchain']
+        whitelist = ['BuildEnv', 'CargoPythonPackage', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage',
+                     'JuliaBundle', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain']
         # Bundles of dependencies without files of their own
         # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore,
         # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co,

From 582b95580d3155a3e4b68100b1cf78d37ca7a4f5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 25 May 2023 10:30:35 +0200
Subject: [PATCH 600/601] add --disable-sphinx for LibTIFF 4.5.0 to avoid
 trouble when Sphinx is available in OS + enhance sanity check

---
 .../easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb  | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb
index 706cc20c7dc..9d9e6c1971c 100644
--- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb
@@ -25,11 +25,14 @@ dependencies = [
 ]
 
 configopts = "--enable-ld-version-script "
-configopts += '--disable-webp'
+configopts += "--disable-webp --disable-sphinx "
 
 sanity_check_paths = {
-    'files': ['bin/tiffinfo'],
+    'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT,
+              'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'],
     'dirs': [],
 }
 
+sanity_check_commands = ["tiffinfo -h"]
+
 moduleclass = 'lib'

From 291deba625e76de62d778248e9076b73f23a131e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 27 May 2023 11:18:58 +0200
Subject: [PATCH 601/601] prepare release notes for EasyBuild v4.7.2 + bump
 version to 4.7.2

---
 RELEASE_NOTES | 94 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 setup.py      |  2 +-
 2 files changed, 94 insertions(+), 2 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index f4454f0b91e..26d8721fa48 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,10 +3,102 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyconfig provides 16,628 easyconfig files, for 2,995 different software packages,
+The latest version of easybuild-easyconfig provides 17,098 easyconfig files, for 3,085 different software packages,
 incl. 39 different (compiler) toolchains.
 
 
+v4.7.2 (27 May 2023)
+--------------------
+
+update/bugfix release
+
+- added easyconfigs for intel/2023.03 (#17676)
+- added example easyconfig files for 89 new software packages:
+  - AGeNT (#17864), anndata (#17677), Annocript (#17910), avro-cpp (#17527), batchgenerators (#17833),
+    BoltzTraP2 (#17742), Braindecode (#17913), build (#17776), casacore (#15499), Casanovo (#17735, #17736),
+    CASPR (#17606), CellChat (#17856), CellOracle (#17507), CLIP (#17782), CodingQuarry (#17682), ColabFold (#17751),
+    CopyKAT (#17646), CPC2 (#17849), cppzmq (#17601), dask-labextension (#17882), DIALOGUE (#17696), DiCE-ML (#17591),
+    ESPResSo (#17709), Evcxr-REPL (#17831), EZC3D (#17832), funannotate (#17588), FunGAP (#17652), GATB-Core (#17635),
+    GenMap (#17746), GimmeMotifs (#17507), GLI (#17793), GOBNILP (#17639), h5netcdf (#17835), HD-BET (#17833),
+    HTSplotter (#17369, #17586), ipympl (#17613), IsoSeq (#17791), KrakenUniq (#17569), LIANA (#17928),
+    libWallModelledLES (#17480), LoRDEC (#17635), M3GNet (#17555), mandrake (#17394), mctc-lib (#16760), MOABB (#17913),
+    MRPRESSO (#17925), ont-guppy (#17477, #17828), OptaDOS (#17777), PALEOMIX (#17912), PGPLOT (#15496),
+    PICI-LIGGGHTS (#17710), pod5-file-format (#17776), powerlaw (#17647), pp-sketchlib (#17397),
+    py3Dmol (#17752), pytesseract (#17898), pytest-cpp (#17966), pytest-flakefinder (#17966), Python-bundle (#17626),
+    python-xxhash (#17844), PyTorch-bundle (#17540), qnorm (#17507), R-MXM (#17667), R-transport (#17642, #17968),
+    Raven (#15833), ReaxFF (#17780), ripunzip (#17959), RPostgreSQL (#17739), rustworkx (#17857), Scalene (#16472),
+    sceasy (#17677), SCIP (#17639), Simple-DFTD3 (#16760), SMAP (#17672), SoPlex (#17639), SoupX (#17851),
+    spektral (#15551), synthcity (#17623), sysbench (#17643), tantan (#17681), thirdorder (#17703), TOPAS (#17553),
+    Triplexator (#17866), tRNAscan-SE (#17680, #17800), turbinesFoam (#17917), unicore-uftp (#17665), vispr (#17606),
+    WCSLIB (#15497), ZIMPL (#17639)
+- added additional easyconfigs for various supported software packages, including:
+  - Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21,
+    Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1,
+    bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11,
+    Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1,
+    CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0,
+    Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0,
+    freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4,
+    googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0,
+    Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5,
+    L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1,
+    libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12,
+    libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4,
+    libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6,
+    mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4,
+    netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0,
+    Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1,
+    pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0,
+    pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0,
+    pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01,
+    ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4,
+    ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1,
+    ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0,
+    Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0,
+    Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5
+- minor enhancements, including:
+  - add local::lib extension to Perl 5.34.0 (#17679)
+  - install shared libraries for tesseract (#17721)
+  - add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (#17738)
+  - add extensions to R-bundle-Bioconductor 3.15: deepSNV (#17852)
+  - add extensions to R 4.2.x: dlm (#17640), PMA + unikn + ppcor (#17695), tvem (#17729), epitools (#17852)
+- various bug fixes, including:
+  - add patch for UCC 1.1.0 for multiple component paths (#17255)
+  - fix configure step for ELSI 2.5.0+ (#17288)
+  - switch bamtofastq to Cargo easyblock (#17595)
+  - add missing OpenJPEG dependency for recent GDAL versions (#17599)
+  - fix CodAn bin/* executable permissions for all users #(#17607)
+  - upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues (#17612)
+  - add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (#17618)
+  - add alternative checksum for MONAI 1.0.1 (#17628)
+  - fix paths to Perl modules in MAKER v3.01.04 (#17629)
+  - add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (#17631)
+  - explicitely disable mpi/python in Boost (intel-compilers/2021.4.0) (#17638)
+  - remove LLVM build dependency from TensorFlow easyconfigs (#17641)
+  - update easyconfig for Longshot 0.4.5 to use Cargo easyblock (#17666)
+  - fix homepage in ELPA easyconfigs (due to switch to new domain) (#17697)
+  - add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (#17713)
+  - use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (#17717)
+  - exclude flaky test_optim for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (#17726, #17730, #17731, #17737)
+  - add missing PCRE dependency for InterProScan 5.55-88.0 (#17762)
+  - fix building Python bindings of DGL, requires static libs (#17764)
+  - only use QEF gitlab source url for QuantumESPRESSO itself (#17766)
+  - add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (#17779)
+  - fix broken source URL for AOCC 4.0.0 (#17794)
+  - specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (#17830)
+  - add Doxygen build dependency to X11 (#17842)
+  - FLINT needs BLAS so move it up from GCC level (#17868)
+  - fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (#17875)
+  - add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (#17887)
+  - add historical repo paths to install cmd for old versions of texlive (#17893)
+  - add missing FastTreeMP binary for FastTree (#17897)
+  - add checksum for arm64 source tarball for Go 1.18.3 (#17903)
+  - add patch to fix test_quantization in PyTorch 1.12.1 (#17908)
+  - add make 4.3 as build dependency for recent OpenBLAS versions (#17924)
+- other changes:
+  - bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775)
+  - move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869)
+
 v4.7.1 (March 20th 2023)
 ------------------------
 
diff --git a/setup.py b/setup.py
index 1e5caaddac1..70004ce1b12 100644
--- a/setup.py
+++ b/setup.py
@@ -44,7 +44,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = '4.7.2.dev0'
+VERSION = '4.7.2'
 
 MAJ_VER = VERSION.split('.')[0]
 MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])