diff options
Diffstat (limited to 'gnu/packages/patches/rsem-makefile.patch')
| -rw-r--r-- | gnu/packages/patches/rsem-makefile.patch | 682 |
1 files changed, 682 insertions, 0 deletions
diff --git a/gnu/packages/patches/rsem-makefile.patch b/gnu/packages/patches/rsem-makefile.patch new file mode 100644 index 0000000000..5481dc685f --- /dev/null +++ b/gnu/packages/patches/rsem-makefile.patch @@ -0,0 +1,682 @@ +This patch simplifies the Makefile, making it much easier to build rsem +without the bundled version of samtools. It has already been submitted +upstream: https://github.com/bli25wisc/RSEM/pull/11 + +From 161894e91a16c7e15af57e4fcfe8cb613711c7fa Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Wed, 22 Apr 2015 14:51:07 +0200 +Subject: [PATCH 1/7] remove all headers from Makefile + +--- + Makefile | 95 +++++++++++----------------------------------------------------- + 1 file changed, 16 insertions(+), 79 deletions(-) + +diff --git a/Makefile b/Makefile +index 54e2603..3a55ed8 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,133 +10,70 @@ all : $(PROGRAMS) + sam/libbam.a : + cd sam ; ${MAKE} all + +-Transcript.h : utils.h +- +-Transcripts.h : utils.h my_assert.h Transcript.h +- +-rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp ++rsem-extract-reference-transcripts : extractRef.cpp + $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts + +-rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp ++rsem-synthesis-reference-transcripts : synthesisRef.cpp + $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts + +-BowtieRefSeqPolicy.h : RefSeqPolicy.h +- +-RefSeq.h : utils.h +- +-Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h +- +- + rsem-preref : preRef.o + $(CC) preRef.o -o rsem-preref + +-preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp ++preRef.o : preRef.cpp + $(CC) $(COFLAGS) preRef.cpp + +- +-SingleRead.h : Read.h +- +-SingleReadQ.h : Read.h +- +-PairedEndRead.h : Read.h SingleRead.h +- +-PairedEndReadQ.h : Read.h SingleReadQ.h +- +- +-PairedEndHit.h : SingleHit.h +- +-HitContainer.h : GroupInfo.h +- +- +-SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h +- +- + rsem-parse-alignments : parseIt.o sam/libbam.a + $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread + +-parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp ++parseIt.o : parseIt.cpp + $(CC) -Wall -O2 -c -I. parseIt.cpp + +- +-rsem-build-read-index : utils.h buildReadIndex.cpp ++rsem-build-read-index : buildReadIndex.cpp + $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index + +- +-simul.h : boost/random.hpp +- +-ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h +- +-SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h +- +-SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h +- +-PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h +- +-PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h +- +-HitWrapper.h : HitContainer.h +- +-sam_rsem_aux.h : sam/bam.h +- +-sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h +- +-BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h +- +-sampling.h : boost/random.hpp +- +-WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h +- + rsem-run-em : EM.o sam/libbam.a + $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread + +-EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp ++EM.o : EM.cpp + $(CC) $(COFLAGS) EM.cpp + +-bc_aux.h : sam/bam.h +- +-BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h +- +-rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a ++rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a + $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ + +-rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp ++rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp + $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ + +-rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp ++rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp + $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ + +-wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h ++wiggle.o: wiggle.cpp + $(CC) $(COFLAGS) wiggle.cpp + + rsem-simulate-reads : simulation.o + $(CC) -o rsem-simulate-reads simulation.o + +-simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp ++simulation.o : simulation.cpp + $(CC) $(COFLAGS) simulation.cpp + + rsem-run-gibbs : Gibbs.o + $(CC) -o rsem-run-gibbs Gibbs.o -lpthread + +-#some header files are omitted +-Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp ++Gibbs.o : Gibbs.cpp + $(CC) $(COFLAGS) Gibbs.cpp + +-Buffer.h : my_assert.h +- + rsem-calculate-credibility-intervals : calcCI.o + $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread + +-#some header files are omitted +-calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp ++calcCI.o : calcCI.cpp + $(CC) $(COFLAGS) calcCI.cpp + +-rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a ++rsem-get-unique : getUnique.cpp sam/libbam.a + $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ + +-rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a ++rsem-sam-validator : samValidator.cpp sam/libbam.a + $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ + +-rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a ++rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a + $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ + + ebseq : + +From ec136638a727632e20abfaeb65c22c46d15ca8c4 Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Wed, 22 Apr 2015 15:06:41 +0200 +Subject: [PATCH 2/7] include current dir, ./sam and ./boost by default + +--- + Makefile | 48 ++++++++++++++++++++++++------------------------ + 1 file changed, 24 insertions(+), 24 deletions(-) + +diff --git a/Makefile b/Makefile +index 3a55ed8..1dd97ca 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,6 @@ + CC = g++ +-CFLAGS = -Wall -c -I. +-COFLAGS = -Wall -O3 -ffast-math -c -I. ++CFLAGS = -Wall -I. -I./sam -I./boost ++COFLAGS = -O3 -ffast-math -c + PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads + + .PHONY : all ebseq clean +@@ -11,70 +11,70 @@ sam/libbam.a : + cd sam ; ${MAKE} all + + rsem-extract-reference-transcripts : extractRef.cpp +- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts ++ $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts + + rsem-synthesis-reference-transcripts : synthesisRef.cpp +- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts ++ $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts + + rsem-preref : preRef.o +- $(CC) preRef.o -o rsem-preref ++ $(CC) $(CFLAGS) preRef.o -o rsem-preref + + preRef.o : preRef.cpp +- $(CC) $(COFLAGS) preRef.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp + + rsem-parse-alignments : parseIt.o sam/libbam.a +- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread ++ $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread + + parseIt.o : parseIt.cpp +- $(CC) -Wall -O2 -c -I. parseIt.cpp ++ $(CC) $(CFLAGS) -O2 -c parseIt.cpp + + rsem-build-read-index : buildReadIndex.cpp +- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index ++ $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index + + rsem-run-em : EM.o sam/libbam.a +- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread ++ $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread + + EM.o : EM.cpp +- $(CC) $(COFLAGS) EM.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) EM.cpp + + rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a +- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ + + rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp +- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ + + rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp +- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ + + wiggle.o: wiggle.cpp +- $(CC) $(COFLAGS) wiggle.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp + + rsem-simulate-reads : simulation.o +- $(CC) -o rsem-simulate-reads simulation.o ++ $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o + + simulation.o : simulation.cpp +- $(CC) $(COFLAGS) simulation.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp + + rsem-run-gibbs : Gibbs.o +- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread ++ $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread + + Gibbs.o : Gibbs.cpp +- $(CC) $(COFLAGS) Gibbs.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp + + rsem-calculate-credibility-intervals : calcCI.o +- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread ++ $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread + + calcCI.o : calcCI.cpp +- $(CC) $(COFLAGS) calcCI.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp + + rsem-get-unique : getUnique.cpp sam/libbam.a +- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@ + + rsem-sam-validator : samValidator.cpp sam/libbam.a +- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@ + + rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a +- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ + + ebseq : + cd EBSeq ; ${MAKE} all + +From d366614ea50f79fdd93e3c76383ccb6fcdeaa8e0 Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Wed, 22 Apr 2015 15:10:49 +0200 +Subject: [PATCH 3/7] separate object rules from rules for executables + +--- + Makefile | 50 ++++++++++++++++++++++++++------------------------ + 1 file changed, 26 insertions(+), 24 deletions(-) + +diff --git a/Makefile b/Makefile +index 1dd97ca..ae4de3b 100644 +--- a/Makefile ++++ b/Makefile +@@ -10,6 +10,32 @@ all : $(PROGRAMS) + sam/libbam.a : + cd sam ; ${MAKE} all + ++ebseq : ++ cd EBSeq ; ${MAKE} all ++ ++ ++calcCI.o : calcCI.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp ++ ++EM.o : EM.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) EM.cpp ++ ++Gibbs.o : Gibbs.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp ++ ++preRef.o : preRef.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp ++ ++parseIt.o : parseIt.cpp ++ $(CC) $(CFLAGS) -O2 -c parseIt.cpp ++ ++simulation.o : simulation.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp ++ ++wiggle.o: wiggle.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp ++ ++ + rsem-extract-reference-transcripts : extractRef.cpp + $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts + +@@ -19,24 +45,15 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp + rsem-preref : preRef.o + $(CC) $(CFLAGS) preRef.o -o rsem-preref + +-preRef.o : preRef.cpp +- $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp +- + rsem-parse-alignments : parseIt.o sam/libbam.a + $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread + +-parseIt.o : parseIt.cpp +- $(CC) $(CFLAGS) -O2 -c parseIt.cpp +- + rsem-build-read-index : buildReadIndex.cpp + $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index + + rsem-run-em : EM.o sam/libbam.a + $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread + +-EM.o : EM.cpp +- $(CC) $(CFLAGS) $(COFLAGS) EM.cpp +- + rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a + $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ + +@@ -46,27 +63,15 @@ rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp + rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp + $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ + +-wiggle.o: wiggle.cpp +- $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp +- + rsem-simulate-reads : simulation.o + $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o + +-simulation.o : simulation.cpp +- $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp +- + rsem-run-gibbs : Gibbs.o + $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread + +-Gibbs.o : Gibbs.cpp +- $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp +- + rsem-calculate-credibility-intervals : calcCI.o + $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread + +-calcCI.o : calcCI.cpp +- $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp +- + rsem-get-unique : getUnique.cpp sam/libbam.a + $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@ + +@@ -76,9 +81,6 @@ rsem-sam-validator : samValidator.cpp sam/libbam.a + rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a + $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ + +-ebseq : +- cd EBSeq ; ${MAKE} all +- + clean : + rm -f *.o *~ $(PROGRAMS) + cd sam ; ${MAKE} clean + +From 6ba1c33cccdf7c8e7df7a3189e7db204be3b1e8d Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Wed, 22 Apr 2015 15:28:30 +0200 +Subject: [PATCH 4/7] add ./sam to library directories, link with -lbam + +--- + Makefile | 36 ++++++++++++++++++------------------ + 1 file changed, 18 insertions(+), 18 deletions(-) + +diff --git a/Makefile b/Makefile +index ae4de3b..a87cc4d 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,11 +1,11 @@ + CC = g++ +-CFLAGS = -Wall -I. -I./sam -I./boost ++CFLAGS = -Wall -I. -I./sam -I./boost -L./sam + COFLAGS = -O3 -ffast-math -c + PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads + + .PHONY : all ebseq clean + +-all : $(PROGRAMS) ++all : sam/libbam.a $(PROGRAMS) + + sam/libbam.a : + cd sam ; ${MAKE} all +@@ -45,23 +45,23 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp + rsem-preref : preRef.o + $(CC) $(CFLAGS) preRef.o -o rsem-preref + +-rsem-parse-alignments : parseIt.o sam/libbam.a +- $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread ++rsem-parse-alignments : parseIt.o ++ $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread + + rsem-build-read-index : buildReadIndex.cpp + $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index + +-rsem-run-em : EM.o sam/libbam.a +- $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread ++rsem-run-em : EM.o ++ $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread + +-rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a +- $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@ ++rsem-tbam2gbam : tbam2gbam.cpp ++ $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@ + +-rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp +- $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++rsem-bam2wig : wiggle.o bam2wig.cpp ++ $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@ + +-rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp +- $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@ ++rsem-bam2readdepth : wiggle.o bam2readdepth.cpp ++ $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@ + + rsem-simulate-reads : simulation.o + $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o +@@ -72,14 +72,14 @@ rsem-run-gibbs : Gibbs.o + rsem-calculate-credibility-intervals : calcCI.o + $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread + +-rsem-get-unique : getUnique.cpp sam/libbam.a +- $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@ ++rsem-get-unique : getUnique.cpp ++ $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@ + +-rsem-sam-validator : samValidator.cpp sam/libbam.a +- $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@ ++rsem-sam-validator : samValidator.cpp ++ $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@ + +-rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a +- $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ ++rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp ++ $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@ + + clean : + rm -f *.o *~ $(PROGRAMS) + +From 5402b88c269df79ee245c1c59e15f3c8282a0220 Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Wed, 22 Apr 2015 15:33:02 +0200 +Subject: [PATCH 5/7] do not repeat target name, use $@ instead + +--- + Makefile | 18 +++++++++--------- + 1 file changed, 9 insertions(+), 9 deletions(-) + +diff --git a/Makefile b/Makefile +index a87cc4d..7ec90a3 100644 +--- a/Makefile ++++ b/Makefile +@@ -37,22 +37,22 @@ wiggle.o: wiggle.cpp + + + rsem-extract-reference-transcripts : extractRef.cpp +- $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts ++ $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@ + + rsem-synthesis-reference-transcripts : synthesisRef.cpp +- $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts ++ $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@ + + rsem-preref : preRef.o +- $(CC) $(CFLAGS) preRef.o -o rsem-preref ++ $(CC) $(CFLAGS) preRef.o -o $@ + + rsem-parse-alignments : parseIt.o +- $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread + + rsem-build-read-index : buildReadIndex.cpp +- $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index ++ $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@ + + rsem-run-em : EM.o +- $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread + + rsem-tbam2gbam : tbam2gbam.cpp + $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@ +@@ -64,13 +64,13 @@ rsem-bam2readdepth : wiggle.o bam2readdepth.cpp + $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@ + + rsem-simulate-reads : simulation.o +- $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o ++ $(CC) $(CFLAGS) -o $@ simulation.o + + rsem-run-gibbs : Gibbs.o +- $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread ++ $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread + + rsem-calculate-credibility-intervals : calcCI.o +- $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread ++ $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread + + rsem-get-unique : getUnique.cpp + $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@ + +From f60784bc7aa303cc825bd87dd3f5d7d26c51bded Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Wed, 22 Apr 2015 15:44:53 +0200 +Subject: [PATCH 6/7] use automatic variables to refer to prerequisites + +--- + Makefile | 44 ++++++++++++++++++++++---------------------- + 1 file changed, 22 insertions(+), 22 deletions(-) + +diff --git a/Makefile b/Makefile +index 7ec90a3..6540d81 100644 +--- a/Makefile ++++ b/Makefile +@@ -15,71 +15,71 @@ ebseq : + + + calcCI.o : calcCI.cpp +- $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) $< + + EM.o : EM.cpp +- $(CC) $(CFLAGS) $(COFLAGS) EM.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) $< + + Gibbs.o : Gibbs.cpp +- $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) $< + + preRef.o : preRef.cpp +- $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) $< + + parseIt.o : parseIt.cpp +- $(CC) $(CFLAGS) -O2 -c parseIt.cpp ++ $(CC) $(CFLAGS) -O2 -c $< + + simulation.o : simulation.cpp +- $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) $< + + wiggle.o: wiggle.cpp +- $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp ++ $(CC) $(CFLAGS) $(COFLAGS) $< + + + rsem-extract-reference-transcripts : extractRef.cpp +- $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@ ++ $(CC) $(CFLAGS) -O3 $< -o $@ + + rsem-synthesis-reference-transcripts : synthesisRef.cpp +- $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@ ++ $(CC) $(CFLAGS) -O3 $< -o $@ + + rsem-preref : preRef.o +- $(CC) $(CFLAGS) preRef.o -o $@ ++ $(CC) $(CFLAGS) $< -o $@ + + rsem-parse-alignments : parseIt.o +- $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread + + rsem-build-read-index : buildReadIndex.cpp +- $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@ ++ $(CC) $(CFLAGS) -O3 $< -o $@ + + rsem-run-em : EM.o +- $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread ++ $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread + + rsem-tbam2gbam : tbam2gbam.cpp +- $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@ + + rsem-bam2wig : wiggle.o bam2wig.cpp +- $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@ + + rsem-bam2readdepth : wiggle.o bam2readdepth.cpp +- $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@ + + rsem-simulate-reads : simulation.o +- $(CC) $(CFLAGS) -o $@ simulation.o ++ $(CC) $(CFLAGS) -o $@ $< + + rsem-run-gibbs : Gibbs.o +- $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread ++ $(CC) $(CFLAGS) -o $@ $< -lpthread + + rsem-calculate-credibility-intervals : calcCI.o +- $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread ++ $(CC) $(CFLAGS) -o $@ $< -lpthread + + rsem-get-unique : getUnique.cpp +- $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@ + + rsem-sam-validator : samValidator.cpp +- $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@ + + rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp +- $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@ + + clean : + rm -f *.o *~ $(PROGRAMS) + +From 0cf9721077f67fb4ca15fdc59cbfbf24a944debd Mon Sep 17 00:00:00 2001 +From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> +Date: Wed, 22 Apr 2015 15:49:19 +0200 +Subject: [PATCH 7/7] split long line + +--- + Makefile | 17 ++++++++++++++++- + 1 file changed, 16 insertions(+), 1 deletion(-) + +diff --git a/Makefile b/Makefile +index 6540d81..0ab04a5 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,22 @@ + CC = g++ + CFLAGS = -Wall -I. -I./sam -I./boost -L./sam + COFLAGS = -O3 -ffast-math -c +-PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads ++PROGRAMS = \ ++ rsem-extract-reference-transcripts \ ++ rsem-synthesis-reference-transcripts \ ++ rsem-preref \ ++ rsem-parse-alignments \ ++ rsem-build-read-index \ ++ rsem-run-em \ ++ rsem-tbam2gbam \ ++ rsem-run-gibbs \ ++ rsem-calculate-credibility-intervals \ ++ rsem-simulate-reads \ ++ rsem-bam2wig \ ++ rsem-get-unique \ ++ rsem-bam2readdepth \ ++ rsem-sam-validator \ ++ rsem-scan-for-paired-end-reads + + .PHONY : all ebseq clean + |