Merge pull request #17567 from easybuilders/4.7.x

release EasyBuild v4.7.1

.github/workflows/linting.yml

@@ -26,3 +26,6 @@ jobs:
 
     - name: Run flake8 to verify PEP8-compliance of Python code
       run: flake8
+
+    - name: Run flake8 to verify PEP8-compliance of Easyconfigs
+      run: flake8 --select W605  --filename '*.eb'

README.rst

@@ -4,7 +4,7 @@
 
 .. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg
 
-`EasyBuild <https://easybuilders.github.io/easybuild>`_ is a software build
+`EasyBuild <https://easybuild.io>`_ is a software build
 and installation framework that allows you to manage (scientific) software
 on High Performance Computing (HPC) systems in an efficient way.
 
@@ -14,7 +14,7 @@ Easyconfig files are used to specify which software to build, which
 version of the software (and its dependencies), which build parameters
 to use (e.g., which compiler toolchain to use), etc.
 
-The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
+The EasyBuild documentation is available at http://docs.easybuild.io/.
 
 The easybuild-easyconfigs package is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see

RELEASE_NOTES

@@ -3,16 +3,145 @@ 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 16,138 easyconfig files, for 2,904 different software packages,
+The latest version of easybuild-easyconfig provides 16,628 easyconfig files, for 2,995 different software packages,
 incl. 39 different (compiler) toolchains.
 
 
+v4.7.1 (March 20th 2023)
+------------------------
+
+update/bugfix release
+
+- added example easyconfig files for 99 new software packages:
+  - astro-tulips (#17263), BA3-SNPS-autotune (#17248), BayesAss3-SNPs (#17247), Block (#27), CatLearn (#14940),
+    CDFlib (#17133), Cellpose (#13703), CheckM-Database (#17462), chemprop (#17261), cimfomfa (#17268), conan (#17326),
+    cooler (#17328), crossguid (#16207), cuSPARSELt (#17141), cython-blis (#17544), DBCSR (#17170), dclone (#17225),
+    DensPart (#17473), Deprecated (#1248), DLPack (#17311), DMLC-Core (#17311), dorado (#17195), duplex-tools (#17497),
+    eQuilibrator (#16812), fastai (#16985), fastjet (#17367), fastjet-contrib (#17377), ffnvcodec (#17271),
+    finder (#1917), flowFDA (#17495), gbasis (#17473), genomepy (#17506), Giotto-Suite (#17207), GKeyll (#16044),
+    GraphDB (#17280), graphviz-python (#17352), grid (#17473), GUSHR (#16905), Health-GPS (#17434), HepMC3 (#17341),
+    HiCMatrix (#17330), Inferelator (#17223), iodata (#17473), irodsfs (#17486), jupyter-contrib-nbextensions (#17270),
+    jupyterlab-lmod (#16563), jupyterlmod (#16563), kb-python (#17260), kineto (#17194), KMCP (#17267),
+    krbalancing (#17325), Lace (#954), LASSO-Python (#17510), libemf (#16188), loomR (#14518), MAKER (#17345),
+    methylartist (#17264), nanoflann (#17311), netMHCII (#9741), NEXUS-CL (#17350), nichenetr (#17524),
+    Parallel-Hashmap (#17311), pdsh (#17139), Perseus (#17210), PfamScan (#17530), Phenoflow (#17495), PIRATE (#17275),
+    PLAMS (#17473), plot1cell (#17498), pybinding (#17137), pyperf (#17063), pyslim (#17150),
+    pytest-rerunfailures (#17295), pytest-shard (#17295), python-louvain (#17207), PyTorch-Ignite (#15491),
+    PyVCF3 (#17519), R2jags (#17226), rapidcsv (#16211), rapidNJ (#17399), Rivet (#17380), rmarkdown (#17189),
+    scArches (#17069), scHiCExplorer (#17334), scib (#17142), SeaView (#17385), silhouetteRank (#17207),
+    siscone (#17342), smfishHmrf (#17207), sparse-neighbors-search (#17329), SpatialDE (#17207), sradownloader (#17188),
+    stardist (#17215), Strainberry (#17522), toil (#17098), vConTACT2 (#17372), VirSorter2 (#17371),
+    vitessce-python (#17472), vitessceR (#17525), YODA (#17343)
+- added additional easyconfigs for various supported software packages, including:
+  - AlphaFold 2.3.0, Anaconda3 2022.10, angsd 0.940, archspec 0.2.0, Armadillo 11.4.3, AUGUSTUS 3.5.0, bcbio-gff 0.7.0,
+    BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Biopython 1.81, BLAT 3.7, Blender 3.4.1,
+    Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0,
+    Cereal 1.3.2, CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8,
+    CUDA 12.1.0, cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6,
+    DIRAC 23.0, dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0,
+    FabIO 0.14.0, FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4,
+    GDAL 3.6.2, GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1,
+    googletest 1.12.1, GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1,
+    h5py 3.8.0, HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2,
+    Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0,
+    imkl-FFTW 2023.0.0, impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5,
+    JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2,
+    Kent_tools 442, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0,
+    libtirpc 1.3.3, libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0,
+    MATIO 1.5.23, MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, MDAnalysis 2.4.2,
+    Miniconda3 22.11.1, mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14,
+    mygene 3.2.2, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1,
+    networkx 3.0, Nextflow 22.10.6, nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0,
+    OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0,
+    PIPITS 3.0, PLINK 2.00a3.7, plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0,
+    presto 1.0.0-20230113, PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2,
+    py-cpuinfo 9.0.0, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0,
+    PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1,
+    QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, R 4.2.2, Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1,
+    ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0,
+    SAMtools 1.17, Scalasca 2.6.1, scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0,
+    snakemake 7.22.0, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1,
+    SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3,
+    Tkinter 3.10.8, tqdm 4.64.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only,
+    Unidecode 1.3.6, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226,
+    Xerces-C++ 3.2.4, XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6
+- minor enhancements, including:
+  - add additional extensions to R 4.2.1 (#17043, #17125, #17224, #17493, #17523)
+  - add additional extensions to Bioconductor 3.15 (#17126, #17315, #17494)
+  - add sanity check command to OpenMolcas v22.10 (#17128)
+  - add Set::Object and Heap::Fibonacci extensions to Perl 5.32.1 (#17151)
+  - add additional extensions to Python 3.10.8 (required for scipy test suite) (#17159)
+  - enhance OpenFold 1.0.1 for standalone usage (#17206)
+  - add SDL2 dependency for FFmpeg 5.0.1 to build ffplay (#17213)
+  - set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs (#17216)
+  - add Devel::Size + Math::Utils extension to recent Perl easyconfigs (#17246, #17466)
+  - combine errors of extension patch check into a single failure (#17286)
+  - add case-insensitive name clash test (#17303)
+  - add ffnvcodec build dependency to all recent FFmpeg easyconfigs (#17316)
+  - use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2022.05 (#17429)
+  - add source URL to cuDNN 8.8 easyconfig (#17439)
+  - add missing zstd dep to Boost (#17482)
+- various bug fixes, including:
+  - fix postinstallcmds and clarify download instructions for netMHC + netMHCpan 4.0a (#9739, #9740)
+  - fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake (#15845)
+  - add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes) (#17077)
+  - fix build of TensorFlow 2.5+ on aarch64 (#17101)
+  - explictely download qe-gipaw source tarball from qe-gipaw GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#17129)
+  - add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug (#17135)
+  - add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (#17140)
+  - fix source URL for p7zip v17.x (#17144)
+  - add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (#17165)
+  - remove dependency on Pillow from scikit-bio v0.5.7 (#17178)
+  - correctly specify path to libfabric installation prefix in PMIx 4.1.0 easyconfig (#17204)
+  - use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API (#17221)
+  - fix CMake print summary for long hostnames for NECI (#17230)
+  - add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b (#17240)
+  - include required stereo_chemical_props.txt for OpenFold 1.0.1 (#17242)
+  - add patch for PAPI 7.0.0 to fix compilation error (#17244)
+  - also update $PERL5LIB for RepeatMasker v4.1.4 (#17245)
+  - add alternative source_url for MariaDB > 10.4 (#17250)
+  - remove use of rysnc in building Kent_tools (#17252)
+  - add missing pkgconf build dependency in recent libxslt easyconfigs (#17254)
+  - add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1 (#17257)
+  - fix postinstallcmds in shovill easyconfigs (#17279)
+  - allow multiple easyconfigs with same name if they differ by CUDA version included in versionsuffix (#17289)
+  - remove duplicate SlamDunk easyconfig using lowercase name (#17301)
+  - use https in homepage + source URL for GenomeThreader 1.7.3 (#17338)
+  - consistently use Check capitailisation (#17351)
+  - add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs (#17356)
+  - fix homepage + source URL for ELPA (due to switch to new domain) (#17357)
+  - fix homepage in ELPA easyconfigs (due to switch to new domain) (#17358)
+  - rename libpsml for consistency with libPSML (#17359)
+  - replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs (#17412)
+  - update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (#17413)
+  - add patch for Qt5 5.12.2 with GCCcore/11.2.0 to fix template bug (#17464)
+  - replace src include path with installation dir for HDF5 (#17469, #17488)
+  - disable Python support for OTF2 v2.2, since we're not including Python 2.x as dependency (#17499)
+  - update homepage and source urls of DFT-D3 (#17528)
+  - use Binary easyblock for ANIcalculator to prevent RPATH sanity check failures (#17536)
+- other changes:
+  - fix invalid escape sequences in easyconfigs by using raw strings (r"...") (#11149)
+  - add exception for ncbi-vdb 3.0.0 dependency variant (#17131)
+  - use proper source tarball instead of cloning GitHub repository for wxWidgets v3.2.1 (#17167)
+  - enable -fPIC in GEOS 3.11.1 (required by GDAL) (#17196)
+  - fix website/docs links in README (#17232)
+  - remove commented out line and delete unused patch for TALON (#17298)
+  - re-enable disabled tests (#17304)
+  - rename MAGMA to MAGMA-gene-analysis to avoid name collision (#17345)
+  - Archive ARB and blasr patch files (#17346)
+  - Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision (#17348)
+  - consistently use NanoFilt capitalisation (#17349)
+  - rename ncl to NEXUS-CL to avoid case-insensitive name clash (#17350)
+  - rename python graphviz to graphviz-python to avoid case-insensitive name clash (#17352)
+  - archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash (#17364)
+
+
 4.7.0 (Janurary 9th 2023)
 -------------------------
 
 feature release
 
-- added easyconfigs for foss/2022a, intel/2022a common toolchains (#16961 and #16962)
+- added easyconfigs for foss/2022b, intel/2022b common toolchains (#16961 and #16962)
   - see also https://docs.easybuild.io/en/latest/Common-toolchains.html
 - added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724)
 - added example easyconfig files for 107 new software packages:

easybuild/easyconfigs/__archive__/a/AFNI/AFNI-20150717-intel-2015a.eb

@@ -43,13 +43,13 @@ skipsteps = ['configure', 'install']
 
 prebuildopts = "cp Makefile.linux_openmp_64 Makefile && "
 buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver
-buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" '
+buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" '
 buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s ' % majpyver
 buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"'
 buildopts += ' INSTALLDIR=%(installdir)s'

easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.10.eb

@@ -25,7 +25,7 @@ dependencies = [
     ('libGLU', '9.0.0'),
 ]
 
-configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
 configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so -DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.so "
 
 builddependencies = [

easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.11.eb

@@ -25,7 +25,7 @@ dependencies = [
     ('libGLU', '9.0.0', '-Mesa-%s' % mesaver),
 ]
 
-configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
 configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
 configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
 

easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb

@@ -26,7 +26,7 @@ dependencies = [
 ]
 
 configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON "
-configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts += r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
 configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
 configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
 

easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb

@@ -44,7 +44,7 @@ modextrapaths = {
 }
 
 # fix shebang line in all provided perl scripts in tools folder
-postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl",
-                   "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"]
+postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env perl|' %(installdir)s/tools/*.pl",
+                   "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env perl|' %(installdir)s/tools/*.pl"]
 
 moduleclass = 'bio'

easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb

@@ -44,7 +44,7 @@ modextrapaths = {
 }
 
 # fix shebang line in all provided perl scripts in tools folder
-postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl",
-                   "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"]
+postinstallcmds = [r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl",
+                   r"sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"]
 
 moduleclass = 'bio'

easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb

@@ -106,7 +106,7 @@ modextrapaths = {
 }
 
 postinstallcmds = [
-    "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
+    r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
     "chmod +x %(installdir)s/*.pl"  # add execution permission
 ]
 

easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb

@@ -104,7 +104,7 @@ modextrapaths = {
 }
 
 postinstallcmds = [
-    "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
+    r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl",  # fix shebang line
     "chmod +x %(installdir)s/*.pl"  # add execution permission
 ]
 

easybuild/easyconfigs/a/AFNI/AFNI-18.1.09-intel-2018a-Python-3.6.4.eb

@@ -42,13 +42,13 @@ start_dir = 'src'
 
 prebuildopts = "cp Makefile.linux_openmp_64 Makefile && "
 buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)sm" '
-buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
-buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" '
+buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" '
+buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" '
 buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm '
 buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"'
 buildopts += ' INSTALLDIR=%(installdir)s'