commit: 49b36caac2597482c792bee0884ae34bea231806 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Feb 19 19:56:01 2022 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Feb 19 19:56:01 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=49b36caa
sci-biology/STAR: unbundle htslib properly Closes: https://bugs.gentoo.org/833770 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/STAR/STAR-2.7.10a.ebuild | 8 + .../STAR/files/STAR-2.7.10a-fix-build-system.patch | 195 +++++++++++++++++++++ 2 files changed, 203 insertions(+) diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild index 6b1c5b15d482..7239efcfe45c 100644 --- a/sci-biology/STAR/STAR-2.7.10a.ebuild +++ b/sci-biology/STAR/STAR-2.7.10a.ebuild @@ -17,6 +17,7 @@ RDEPEND="sci-libs/htslib:=" DEPEND="${RDEPEND}" BDEPEND="virtual/pkgconfig" +PATCHES=( "${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch ) DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf ) pkg_pretend() { @@ -27,6 +28,13 @@ pkg_setup() { [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp } +src_prepare() { + default + + # remove bundled htslib + rm -r source/htslib || die +} + src_configure() { tc-export CC CXX PKG_CONFIG } diff --git a/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch new file mode 100644 index 000000000000..0f06c94fb109 --- /dev/null +++ b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch @@ -0,0 +1,195 @@ +--- a/source/bam_cat.c ++++ b/source/bam_cat.c +@@ -52,8 +52,8 @@ + #include <stdlib.h> + #include <unistd.h> + +-#include "htslib/htslib/bgzf.h" +-#include "htslib/htslib/sam.h" ++#include <htslib/bgzf.h> ++#include <htslib/sam.h> + #include <cstring> + + #define BUF_SIZE 0x10000 +--- a/source/bam_cat.h ++++ b/source/bam_cat.h +@@ -1,7 +1,7 @@ + #ifndef CODE_bam_cat + #define CODE_bam_cat + +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + + int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam); + +--- a/source/BAMfunctions.cpp ++++ b/source/BAMfunctions.cpp +@@ -1,5 +1,5 @@ + #include "BAMfunctions.h" +-#include "htslib/htslib/kstring.h" ++#include <htslib/kstring.h> + + + string bam_cigarString (bam1_t *b) {//output CIGAR string +--- a/source/bamRemoveDuplicates.cpp ++++ b/source/bamRemoveDuplicates.cpp +@@ -1,7 +1,7 @@ + #include <unordered_map> + #include "bamRemoveDuplicates.h" + #include <iostream> +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + #include "IncludeDefine.h" + #include SAMTOOLS_BGZF_H + #include "ErrorWarning.h" +--- a/source/IncludeDefine.h ++++ b/source/IncludeDefine.h +@@ -30,8 +30,8 @@ + #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ ) + + //external libs +-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h" +-#define SAMTOOLS_SAM_H "htslib/htslib/sam.h" ++#define SAMTOOLS_BGZF_H <htslib/bgzf.h> ++#define SAMTOOLS_SAM_H <htslib/sam.h> + + using namespace std; + +--- a/source/Makefile ++++ b/source/Makefile +@@ -12,11 +12,7 @@ + CXX ?= g++ + + # pre-defined flags +-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz +-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz +-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a +-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a +-LDFLAGS_gdb := $(LDFLAGS_shared) ++LIBS := -pthread -lhts -lz + + DATE_FMT = --iso-8601=seconds + ifdef SOURCE_DATE_EPOCH +@@ -27,7 +23,7 @@ + + BUILD_PLACE ?= $(HOSTNAME):$(shell pwd) + +-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"' ++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""' + + + GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0) +@@ -41,13 +37,13 @@ + + # Defaults, can be overridden by make arguments or environment + CXXFLAGS ?= -pipe -Wall -Wextra +-CFLAGS ?= -pipe -Wall -Wextra -O3 ++CFLAGS ?= -pipe -Wall -Wextra + CXXFLAGS_SIMD ?= -mavx2 + + # Unconditionally set essential flags and optimization options + CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF) +-CXXFLAGS_main := -O3 $(CXXFLAGS_common) +-CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common) ++CXXFLAGS_main := $(CXXFLAGS_common) ++CXXFLAGS_gdb := $(CXXFLAGS_common) + + ########################################################################################################## + OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \ +@@ -130,7 +126,7 @@ + ifneq ($(MAKECMDGOALS),clean_solo) + ifneq ($(MAKECMDGOALS),STARforMac) + ifneq ($(MAKECMDGOALS),STARforMacGDB) +-Depend.list: $(SOURCES) parametersDefault.xxd htslib ++Depend.list: $(SOURCES) parametersDefault.xxd + echo $(SOURCES) + 'rm' -f ./Depend.list + $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list +@@ -142,57 +138,43 @@ + endif + endif + +-htslib : htslib/libhts.a +- +-htslib/libhts.a : +- $(MAKE) -C htslib lib-static +- + parametersDefault.xxd: parametersDefault + xxd -i parametersDefault > parametersDefault.xxd + + STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) +-STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) + STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS) +-STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) + STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) +-STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) + STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) +-STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS) + STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + + + POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS) +-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS) + POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS) + + gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS) +-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) + gdb : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS) + + gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS) +-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS) + gdb-long : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) +-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) + STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS) + + STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS) +-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS) + STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS) +- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS) ++ $(CXX) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS) +--- a/source/signalFromBAM.h ++++ b/source/signalFromBAM.h +@@ -1,6 +1,6 @@ + #ifndef CODE_signalFromBAM + #define CODE_signalFromBAM +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + #include <fstream> + #include <string> + #include "Stats.h" +--- a/source/STAR.cpp ++++ b/source/STAR.cpp +@@ -29,7 +29,7 @@ + + #include "twoPassRunPass1.h" + +-#include "htslib/htslib/sam.h" ++#include <htslib/sam.h> + #include "parametersDefault.xxd" + + void usage(int usageType) {
