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 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 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 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 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 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 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 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