From: Bo Li Date: Sun, 8 Jun 2014 00:45:27 +0000 (-0500) Subject: Renamed makefile as Makefile X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=412c1a2821c5a4cbe2e68e4e9f4e2026a86d25f7;ds=sidebyside Renamed makefile as Makefile --- diff --git a/EBSeq/Makefile b/EBSeq/Makefile new file mode 100644 index 0000000..78b6d60 --- /dev/null +++ b/EBSeq/Makefile @@ -0,0 +1,15 @@ +CC = g++ +PROGRAMS = EBSeq rsem-for-ebseq-calculate-clustering-info + +.PHONY : all EBSeq clean + +all : $(PROGRAMS) + +EBSeq : + ./install + +rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp + $(CC) -O3 -Wall calcClusteringInfo.cpp -o $@ + +clean : + rm -rf blockmodeling $(PROGRAMS) *~ BiocInstaller diff --git a/EBSeq/makefile b/EBSeq/makefile deleted file mode 100644 index 898c8fa..0000000 --- a/EBSeq/makefile +++ /dev/null @@ -1,13 +0,0 @@ -CC = g++ -PROGRAMS = EBSeq rsem-for-ebseq-calculate-clustering-info - -all : $(PROGRAMS) - -EBSeq : - ./install - -rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp - $(CC) -O3 -Wall calcClusteringInfo.cpp -o $@ - -clean : - rm -rf blockmodeling $(PROGRAMS) *~ BiocInstaller diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..a9a705f --- /dev/null +++ b/Makefile @@ -0,0 +1,148 @@ +CC = g++ +CFLAGS = -Wall -c -I. +COFLAGS = -Wall -O3 -ffast-math -c -I. +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) + +sam/libbam.a : + cd sam ; ${MAKE} all + +Transcript.h : utils.h + +Transcripts.h : my_assert.h Transcript.h + +rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h 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 + $(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 + $(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 + $(CC) -Wall -O2 -c -I. parseIt.cpp + + +rsem-build-read-index : utils.h 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 + $(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 + $(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 + $(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 + $(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 + $(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 + $(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 + $(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 + $(CC) $(COFLAGS) calcCI.cpp + +rsem-get-unique : sam/bam.h sam/sam.h 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 + $(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 + $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ + +ebseq : + cd EBSeq ; ${MAKE} all + +clean : + rm -f *.o *~ $(PROGRAMS) + cd sam ; ${MAKE} clean + cd EBSeq ; ${MAKE} clean diff --git a/makefile b/makefile deleted file mode 100644 index 76e1ac3..0000000 --- a/makefile +++ /dev/null @@ -1,148 +0,0 @@ -CC = g++ -CFLAGS = -Wall -c -I. -COFLAGS = -Wall -O3 -ffast-math -c -I. -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 - -all : $(PROGRAMS) - -sam/libbam.a : - cd sam ; ${MAKE} all - -Transcript.h : utils.h - -Transcripts.h : my_assert.h Transcript.h - -rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h 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 - $(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 - $(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 - $(CC) -Wall -O2 -c -I. parseIt.cpp - - -rsem-build-read-index : utils.h 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 - $(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 - $(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 - $(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 - $(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 - $(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 - $(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 - $(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 - $(CC) $(COFLAGS) calcCI.cpp - -rsem-get-unique : sam/bam.h sam/sam.h 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 - $(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 - $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ - -.PHONY: ebseq - -ebseq : - cd EBSeq ; ${MAKE} all - -clean : - rm -f *.o *~ $(PROGRAMS) - cd sam ; ${MAKE} clean - cd EBSeq ; ${MAKE} clean