forked from Lainports/freebsd-ports
biology/star: Update to 2.7.9a
Also unbundle htslib Changes: https://github.com/alexdobin/STAR/releases/tag/2.7.9a
This commit is contained in:
Jason W. Bacon
parent
81c7eb4553
commit
869afa4fe6
8 changed files with 162 additions and 35 deletions
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@ -1,6 +1,5 @@
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PORTNAME= STAR
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DISTVERSION= 2.7.3a
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PORTREVISION= 1
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DISTVERSION= 2.7.9a
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CATEGORIES= biology
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PKGNAMEPREFIX= rna-
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@ -10,17 +9,34 @@ COMMENT= Spliced Transcripts Alignment to a Reference
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LICENSE= GPLv3
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LICENSE_FILE= ${WRKDIR}/STAR-${DISTVERSION}/LICENSE
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# 64-bit only, needs 16+ GiB RAM for typical eukaryotic genome
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NOT_FOR_ARCHS= i386 powerpc
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NOT_FOR_ARCHS_REASON=Needs 16+ GiB RAM for typical eukaryotic genome
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USES= compiler:c++11-lang gmake
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LIB_DEPENDS= libhts.so:biology/htslib
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USES= compiler:c++11-lang gmake localbase:ldflags
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USE_GITHUB= yes
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GH_ACCOUNT= alexdobin
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WRKSRC_SUBDIR= source
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MAKE_FLAGS= HTSLIB=''
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PLIST_FILES= bin/STAR
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post-patch:
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${RM} -rf ${WRKSRC}/htslib
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${REINPLACE_CMD} \
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-e 's|"htslib/htslib/sam.h"|<htslib/sam.h>|g' \
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-e 's|"htslib/htslib/kstring.h"|<htslib/kstring.h>|g' \
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-e 's|"htslib/htslib/bgzf.h"|<htslib/bgzf.h>|g' \
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${WRKSRC}/BAMfunctions.cpp \
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${WRKSRC}/IncludeDefine.h \
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${WRKSRC}/STAR.cpp \
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${WRKSRC}/bamRemoveDuplicates.cpp \
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${WRKSRC}/bam_cat.c \
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${WRKSRC}/bam_cat.h \
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${WRKSRC}/signalFromBAM.h
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do-install:
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${INSTALL_PROGRAM} ${WRKSRC}/STAR ${STAGEDIR}${PREFIX}/bin
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@ -1,3 +1,3 @@
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TIMESTAMP = 1586376571
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SHA256 (alexdobin-STAR-2.7.3a_GH0.tar.gz) = de204175351dc5f5ecc40cf458f224617654bdb8e00df55f0bb03a5727bf26f9
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SIZE (alexdobin-STAR-2.7.3a_GH0.tar.gz) = 8550987
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TIMESTAMP = 1637942811
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SHA256 (alexdobin-STAR-2.7.9a_GH0.tar.gz) = ff52c9d6daaa9fb7261efa3aa49ef6ce5262aa089b0762a3cbc751e81321050e
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SIZE (alexdobin-STAR-2.7.9a_GH0.tar.gz) = 10669338
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@ -1,23 +1,61 @@
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--- Makefile.orig 2019-10-08 19:10:51 UTC
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--- Makefile.orig 2021-05-05 12:01:50 UTC
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+++ Makefile
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@@ -20,11 +20,16 @@ LDFLAGS_gdb := $(LDFLAGS_shared)
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@@ -11,6 +11,10 @@ CXXFLAGSextra ?=
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# user may define the compiler
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CXX ?= g++
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COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
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-CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
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-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
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-CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common)
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+# Defaults, overridden by make arguments or environment
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+CXXFLAGS ?= -pipe -O3 -Wall -Wextra
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+CFLAGS ?= -pipe -O3 -Wall -Wextra
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-CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
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+# Unconditionally set essential flags
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+CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE)
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+CXXFLAGS_main += $(CXXFLAGS_common)
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+# user may set to '' and sed "htslib/htslib/*.h" to <htslib/*.h>
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+# if they don't want the bundled htslib
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+HTSLIB ?= htslib
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+
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+# -O or -O2 should work fine with gdb as well
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+CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common)
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# pre-defined flags
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LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
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LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
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@@ -18,7 +22,8 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
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LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
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LDFLAGS_gdb := $(LDFLAGS_shared)
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-DATE_FMT = --iso-8601=seconds
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+# --iso-8601 is not portable
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+DATE_FMT = -Iseconds
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ifdef SOURCE_DATE_EPOCH
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BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)")
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else
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@@ -30,13 +35,13 @@ BUILD_PLACE ?= $(HOSTNAME):$(shell pwd)
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COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"'
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# Defaults, can be overridden by make arguments or environment
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-CXXFLAGS ?= -pipe -Wall -Wextra
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+CXXFLAGS ?= -pipe -Wall -Wextra -O3
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CFLAGS ?= -pipe -Wall -Wextra -O3
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CXXFLAGS_SIMD ?= -mavx2
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# Unconditionally set essential flags and optimization options
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CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE)
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-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
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+CXXFLAGS_main := $(CXXFLAGS_common)
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CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
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##########################################################################################################
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@@ -102,7 +107,7 @@ clean:
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.PHONY: CLEAN
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CLEAN: clean
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- $(MAKE) -C htslib clean
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+ $(MAKE) -C $(HTSLIB) clean
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.PHONY: clean_solo
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@@ -119,10 +124,10 @@ ifneq ($(MAKECMDGOALS),CLEAN)
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ifneq ($(MAKECMDGOALS),clean_solo)
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ifneq ($(MAKECMDGOALS),STARforMac)
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ifneq ($(MAKECMDGOALS),STARforMacGDB)
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-Depend.list: $(SOURCES) parametersDefault.xxd htslib
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+Depend.list: $(SOURCES) parametersDefault.xxd $(HTSLIB)
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echo $(SOURCES)
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'rm' -f ./Depend.list
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- $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
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+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) -MM $^ >> Depend.list
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include Depend.list
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endif
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endif
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@ -1,11 +0,0 @@
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--- SharedMemory.cpp.orig 2019-04-21 19:57:39 UTC
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+++ SharedMemory.cpp
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@@ -11,7 +11,7 @@
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#include <semaphore.h>
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#include <errno.h>
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-#ifdef COMPILE_FOR_MAC
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+#if defined(COMPILE_FOR_MAC) || defined(__FreeBSD__)
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//some Mac's idiosyncrasies: standard SHM libraries are very old and missing some definitions
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#define SHM_NORESERVE 0
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#endif
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10
biology/star/files/patch-SpliceGraph.cpp
Normal file
10
biology/star/files/patch-SpliceGraph.cpp
Normal file
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@ -0,0 +1,10 @@
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--- SpliceGraph.cpp.orig 2021-11-26 18:13:48 UTC
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+++ SpliceGraph.cpp
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@@ -1,7 +1,6 @@
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/*
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* Created by Fahimeh Mirhaj on 6/10/19.
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*/
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-using namespace std;
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#include "SpliceGraph.h"
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#include "GTF.h"
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50
biology/star/files/patch-SuffixArrayFuns.cpp
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50
biology/star/files/patch-SuffixArrayFuns.cpp
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@ -0,0 +1,50 @@
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--- SuffixArrayFuns.cpp.orig 2021-11-26 18:14:36 UTC
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+++ SuffixArrayFuns.cpp
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@@ -15,7 +15,7 @@ uint compareSeqToGenome(Genome &mapGen, char** s2, uin
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* dirR forward or reverse direction search on read sequence
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*/
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- register int64 ii;
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+ int64 ii;
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uint SAstr=mapGen.SA[iSA];
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bool dirG = (SAstr>>mapGen.GstrandBit) == 0; //forward or reverse strand of the genome
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@@ -231,7 +231,7 @@ uint compareSeqToGenome1(Genome &mapGen, char** s2, ui
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//TODO no need for complementary sequence
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- register int64 ii;
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+ int64 ii;
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uint SAstr=mapGen.SA[iSA];
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bool dirG = (SAstr>>mapGen.GstrandBit) == 0; //forward or reverse strand of the genome
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@@ -356,13 +356,13 @@ uint funCalcSAiFromSA(char* gSeq, PackedArray& gSA, Ge
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bool dirG = (SAstr>>mapGen.GstrandBit) == 0; //forward or reverse strand of the genome
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SAstr &= mapGen.GstrandMask;
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iL4=-1;
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- register uint saind=0;
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+ uint saind=0;
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if (dirG)
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{
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- register uint128 g1=*( (uint128*) (gSeq+SAstr) );
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+ uint128 g1=*( (uint128*) (gSeq+SAstr) );
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for (int ii=0; ii<L; ii++)
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{
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- register char g2=(char) g1;
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+ char g2=(char) g1;
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if (g2>3)
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{
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iL4=ii;
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@@ -376,10 +376,10 @@ uint funCalcSAiFromSA(char* gSeq, PackedArray& gSA, Ge
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return saind;
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} else
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{
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- register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) );
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+ uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) );
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for (int ii=0; ii<L; ii++)
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{
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- register char g2=(char) (g1>>(8*(15-ii)));
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+ char g2=(char) (g1>>(8*(15-ii)));
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if (g2>3)
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{
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iL4=ii;
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11
biology/star/files/patch-bamSortByCoordinate.cpp
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11
biology/star/files/patch-bamSortByCoordinate.cpp
Normal file
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@ -0,0 +1,11 @@
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--- bamSortByCoordinate.cpp.orig 2021-11-26 16:17:37 UTC
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+++ bamSortByCoordinate.cpp
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@@ -64,7 +64,7 @@ void bamSortByCoordinate (Parameters &P, ReadAlignChun
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boolWait=false;
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totalMem+=newMem;
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};
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- sleep(0.1);
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+ usleep(10000);
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};
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BAMbinSortByCoordinate(ibin,binN,binS,P.runThreadN,P.outBAMsortTmpDir, P, genome, solo);
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#pragma omp critical
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13
biology/star/files/patch-opal_opal.cpp
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13
biology/star/files/patch-opal_opal.cpp
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@ -0,0 +1,13 @@
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--- opal/opal.cpp.orig 2021-11-26 16:14:46 UTC
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+++ opal/opal.cpp
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@@ -5,10 +5,8 @@
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#include <limits>
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#include <vector>
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-extern "C" {
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#define SIMDE_ENABLE_NATIVE_ALIASES
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#include <simde_avx2.h> // AVX2 and lower
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-}
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#include "opal.h"
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