From 4cbcc855382a06088e2f016f62cafdbcb7e40665 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 20 Mar 2022 00:40:44 +0000 Subject: gentoo resync : 20.03.2022 --- sci-biology/STAR/Manifest | 3 + sci-biology/STAR/STAR-2.7.10a.ebuild | 49 ++++++ .../STAR/files/STAR-2.7.10a-fix-build-system.patch | 195 +++++++++++++++++++++ 3 files changed, 247 insertions(+) create mode 100644 sci-biology/STAR/STAR-2.7.10a.ebuild create mode 100644 sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch (limited to 'sci-biology/STAR') diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest index 3fb4a0879865..8f7c05fc8c7f 100644 --- a/sci-biology/STAR/Manifest +++ b/sci-biology/STAR/Manifest @@ -1,4 +1,7 @@ AUX STAR-2.5.3a-fix-build-system.patch 5318 BLAKE2B 28a839eb61a5b1adef804249328c7917dca2ec765f00a48b90aa42d7da3ca393f7726b7aafdb6d0429a55fe696bd51b0e06d85ef6e50a3a4f5874c731b194f1e SHA512 412bdf74c50869f470f3d7452d3799e92a45da198e50ecad63688e4c24444a25f044d464e462e19ba41c5abf590865e43542cd1b60a1f3948bf357be468e8441 +AUX STAR-2.7.10a-fix-build-system.patch 7176 BLAKE2B 24a14d2d8af26565a3a7f754e9633c54c2cdaf72bf4e3b4fe3390a3790be16620117f576abf82d91e8816478fc1a012e7424ab6d93bb6161b975acd08627d3f0 SHA512 4d854336b2e0c61ca1ac604cded7f08e484974e1ec6d78928e5eb21eb7adb0ae3f6ec9deb3dc050dcffe1732f9076f2b4cddad7aa18ccad20f9232c9e11d1856 DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf +DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9 EBUILD STAR-2.5.3a.ebuild 881 BLAKE2B 692466b512aaa3da2e2323f90576d47c2f5e694a4ac8ee8ce2d887435a1ef964dcab9adbdb3c3f88b43cc5463b258635be0f2b542485ee16bc9ec32b655fcf65 SHA512 9b8a80c19b0da8e697c913a8401c08a71a07511477c71b1dd20748e5487e8bb5ab870c37058d49abc27a5ac56722e98b2d784431c19f7173275b82f41f9a2663 +EBUILD STAR-2.7.10a.ebuild 970 BLAKE2B 63bc2b4656d4e672faf819f83bd2a930851e0b5c2d1ff422c5a72b655d5c68515a317675c59df2ff9256e4653351f1f180d9c94dbd256c89810d31ca3940b9ad SHA512 76841ebb6bb3a7c15da15c2124287959938beeb1c6e1a5fa362c476283b51dca49bcca83be9e10d5f39702f23b01ee131f8ab2f568b986e529fc006e65a25ffb MISC metadata.xml 341 BLAKE2B 5cf54dcbc5013bbebd80edd8d03456553ec6f7f52527d076f921916ebe9b862c97aae6f641741b81ac44cfc84356ca13e19dd3be2b63c075923a701c22e695c1 SHA512 888d00d5873390206f21aa9daaf78fc8c3f9b88e528c38ca7696779b221fd21acc6beadf543c14e16f74cb600cab479bc3f9bba8625214480583f369e6ea67a8 diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild new file mode 100644 index 000000000000..7239efcfe45c --- /dev/null +++ b/sci-biology/STAR/STAR-2.7.10a.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays" +HOMEPAGE="https://github.com/alexdobin/STAR" +SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND="sci-libs/htslib:=" +DEPEND="${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() { + [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp +} + +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 +} + +src_compile() { + emake -C source STAR +} + +src_install() { + dobin source/STAR + einstalldocs +} 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 + #include + +-#include "htslib/htslib/bgzf.h" +-#include "htslib/htslib/sam.h" ++#include ++#include + #include + + #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 + + 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 + + + string bam_cigarString (bam1_t *b) {//output CIGAR string +--- a/source/bamRemoveDuplicates.cpp ++++ b/source/bamRemoveDuplicates.cpp +@@ -1,7 +1,7 @@ + #include + #include "bamRemoveDuplicates.h" + #include +-#include "htslib/htslib/sam.h" ++#include + #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 ++#define SAMTOOLS_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 + #include + #include + #include "Stats.h" +--- a/source/STAR.cpp ++++ b/source/STAR.cpp +@@ -29,7 +29,7 @@ + + #include "twoPassRunPass1.h" + +-#include "htslib/htslib/sam.h" ++#include + #include "parametersDefault.xxd" + + void usage(int usageType) { -- cgit v1.2.3