Rebuild stringtie on osx

bioconda · Dec 13, 2024 · 9191c9b · 9191c9b
1 parent 3f1de47
commit 9191c9b
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Showing 3 changed files with 33 additions and 11 deletions.
diff --git a/recipes/stringtie/build.sh b/recipes/stringtie/build.sh
@@ -1,16 +1,24 @@
 #!/bin/bash
 
+mkdir -p $PREFIX/bin
 ln -sf $PREFIX/lib/libz.so.1 $PREFIX/lib/libz.so
 
 export C_INCLUDE_PATH=$PREFIX/include
 export CPLUS_INCLUDE_PATH=$PREFIX/include
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export LINKER="$CXX"
 export CXXFLAGS="$CPPFLAGS"
 
-make release CXX=$CXX
-mkdir -p $PREFIX/bin
-chmod 755 stringtie
-mv stringtie $PREFIX/bin
+cd SuperReads_RNA/global-1
+autoreconf -if
+./configure CC="${CC}" CXX="${CXX}" LDFLAGS="${LDFLAGS}"
+cd ../../htslib
+autoreconf -if
+./configure CC="${CC}" CXX="${CXX}" LDFLAGS="${LDFLAGS}"
+cd ../
+
+make release CXX="${CXX}" LINKER="${CXX}" -j"${CPU_COUNT}"
+install -v -m 0755 stringtie $PREFIX/bin
 
 # Prepare prepDE
 # This is equivalent to https://github.com/gpertea/stringtie/blob/master/prepDE.py

diff --git a/recipes/stringtie/meta.yaml b/recipes/stringtie/meta.yaml
@@ -13,10 +13,7 @@ source:
     - patch
 
 build:
-  number: 0
-  # TODO currently fails to build on osx.
-  # Feel free to re-enable and debug.
-  skip: True  # [osx]
+  number: 1
   run_exports:
     - {{ pin_subpackage("stringtie", max_pin="x") }}
 
@@ -25,10 +22,11 @@ requirements:
     - make
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - zlib
   host:
     # curl is used to download prepDE.py
     - htslib
+    - curl
+    - zlib
   run:
     - htslib
     - python
@@ -50,6 +48,7 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:stringtie
     - usegalaxy-eu:stringtie

diff --git a/recipes/stringtie/patch b/recipes/stringtie/patch
@@ -1,5 +1,5 @@
 diff --git a/Makefile b/Makefile
-index d7b179e..a54e396 100644
+index d29c461..0eb9c6b 100644
 --- a/Makefile
 +++ b/Makefile
 @@ -1,5 +1,5 @@
@@ -9,6 +9,21 @@ index d7b179e..a54e396 100644
  #-- 
  LIBDEFLATE := ${HTSLIB}/xlibs/lib/libdeflate.a
  LIBBZ2 := ${HTSLIB}/xlibs/lib/libbz2.a
+@@ -8,12 +8,12 @@ LIBLZMA := ${HTSLIB}/xlibs/lib/liblzma.a
+ GDIR := ./gclib
+ #--
+
+-INCDIRS := -I. -I${GDIR} -I${HTSLIB}
++INCDIRS := -I. -I${GDIR} -I${HTSLIB} -I${PREFIX}/include
+
+ CXX   := $(if $(CXX),$(CXX),g++)
+
+ BASEFLAGS := -Wall -Wextra ${INCDIRS} -fsigned-char -D_FILE_OFFSET_BITS=64 \
+--D_LARGEFILE_SOURCE -std=c++11 -fno-strict-aliasing -fno-exceptions -fno-rtti
++-D_LARGEFILE_SOURCE -std=c++14 -fno-strict-aliasing -fno-exceptions -fno-rtti
+ #for gcc 8+ add: -Wno-class-memaccess
+ GCCGTE5 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 5)
+ ifeq "$(GCCGTE5)" "1"
 @@ -31,7 +31,7 @@ LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
 
  # LDFLAGS += -L${BAM}
@@ -18,7 +33,7 @@ index d7b179e..a54e396 100644
 
  ifneq (,$(filter %nothreads %prof %profile, $(MAKECMDGOALS)))
   NOTHREADS=1
-@@ -172,10 +172,7 @@ tablemaker.o : tablemaker.h rlink.h
+@@ -170,10 +170,7 @@ tablemaker.o : tablemaker.h rlink.h
  ##${BAM}/libbam.a: 
  ##	cd ${BAM} && make lib