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|
SAMTOOLS = samtools-1.3
HTSLIB = htslib-1.3
ifneq ($(cygwin), true)
SAMTOOLS_MAKEFILE = Makefile
else
SAMTOOLS_MAKEFILE = Makefile.cygwin
endif
# overridable, defaulting to local copy
BOOST = .
# Compilation variables
CXX = g++
CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST)
CPPFLAGS ?=
LDFLAGS ?=
LDLIBS ?=
# Installation variables
INSTALL = install
INSTALL_PROGRAM = $(INSTALL) -p
INSTALL_DATA = $(INSTALL) -p -m 644
INSTALL_DIR = $(INSTALL) -d
STRIP ?=strip
prefix ?= /usr/local
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
# Auxiliary variables for compilation
SAMHEADERS =
SAMLIBS =
CONFIGURE = ./configure
OBJS1 = parseIt.o
OBJS2 = extractRef.o synthesisRef.o preRef.o buildReadIndex.o wiggle.o tbam2gbam.o bam2wig.o bam2readdepth.o getUnique.o samValidator.o scanForPairedEndReads.o SamHeader.o
OBJS3 = EM.o Gibbs.o calcCI.o simulation.o
PROGS1 = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index rsem-simulate-reads
PROGS2 = rsem-parse-alignments rsem-run-em rsem-tbam2gbam rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator rsem-scan-for-paired-end-reads
PROGS3 = rsem-run-gibbs rsem-calculate-credibility-intervals
PROGRAMS = $(PROGS1) $(PROGS2) $(PROGS3)
# Auxiliary variables for installation
SCRIPTS = rsem-prepare-reference rsem-calculate-expression rsem-refseq-extract-primary-assembly rsem-gff3-to-gtf rsem-plot-model \
rsem-plot-transcript-wiggles rsem-gen-transcript-plots rsem-generate-data-matrix \
extract-transcript-to-gene-map-from-trinity convert-sam-for-rsem
.PHONY : all ebseq pRSEM clean
all : $(PROGRAMS)
$(SAMTOOLS)/samtools :
cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools
$(SAMLIBS) :
# Compile objects
$(OBJS1) :
$(CXX) $(CXXFLAGS) $(CPPFLAGS) -O2 -c -o $@ $<
$(OBJS2) :
$(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -c -o $@ $<
$(OBJS3) :
$(CXX) $(CXXFLAGS) $(CPPFLAGS) -O3 -ffast-math -c -o $@ $<
# Generate executables
$(PROGS1) :
$(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS)
$(PROGS2) :
$(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lhts -lz
$(PROGS3) :
$(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lhts
# Dependencies for executables
rsem-extract-reference-transcripts : extractRef.o
rsem-synthesis-reference-transcripts : synthesisRef.o
rsem-preref : preRef.o
rsem-build-read-index : buildReadIndex.o
rsem-simulate-reads : simulation.o
rsem-parse-alignments : parseIt.o $(SAMLIBS)
rsem-run-em : EM.o SamHeader.o $(SAMLIBS)
rsem-tbam2gbam : tbam2gbam.o SamHeader.o $(SAMLIBS)
rsem-bam2wig : bam2wig.o wiggle.o $(SAMLIBS)
rsem-bam2readdepth : bam2readdepth.o wiggle.o $(SAMLIBS)
rsem-get-unique : getUnique.o $(SAMLIBS)
rsem-sam-validator : samValidator.o $(SAMLIBS)
rsem-scan-for-paired-end-reads : scanForPairedEndReads.o $(SAMLIBS)
rsem-run-gibbs : Gibbs.o
rsem-calculate-credibility-intervals : calcCI.o
# Dependencies for objects
parseIt.o : parseIt.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h
extractRef.o : extractRef.cpp utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h
synthesisRef.o : synthesisRef.cpp utils.h my_assert.h Transcript.h Transcripts.h
preRef.o : preRef.cpp utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h
buildReadIndex.o : buildReadIndex.cpp utils.h
wiggle.o: wiggle.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h wiggle.h
tbam2gbam.o : tbam2gbam.cpp $(SAMHEADERS) utils.h Transcripts.h Transcript.h BamConverter.h sam_utils.h SamHeader.hpp my_assert.h bc_aux.h
bam2wig.o : bam2wig.cpp utils.h my_assert.h wiggle.h
bam2readdepth.o : bam2readdepth.cpp utils.h my_assert.h wiggle.h
getUnique.o : getUnique.cpp $(SAMHEADERS) sam_utils.h utils.h
samValidator.o : samValidator.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h
scanForPairedEndReads.o : scanForPairedEndReads.cpp $(SAMHEADERS) sam_utils.h utils.h my_assert.h
SamHeader.o : SamHeader.cpp $(SAMHEADERS) SamHeader.hpp
EM.o : EM.cpp $(SAMHEADERS) 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 simul.h sam_utils.h SamHeader.hpp sampling.h $(BOOST)/boost/random.hpp WriteResults.h
Gibbs.o : Gibbs.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h
calcCI.o : calcCI.cpp utils.h my_assert.h $(BOOST)/boost/random.hpp sampling.h simul.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h ModelParams.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
simulation.o : simulation.cpp 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)/boost/random.hpp WriteResults.h
# Dependencies for header files
Transcript.h : utils.h
Transcripts.h : utils.h my_assert.h Transcript.h
BowtieRefSeqPolicy.h : RefSeqPolicy.h
RefSeq.h : utils.h
Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
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
sam_utils.h : $(SAMHEADERS) Transcript.h Transcripts.h
SamParser.h : $(SAMHEADERS) sam_utils.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
simul.h : $(BOOST)/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
BamWriter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
sampling.h : $(BOOST)/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
bc_aux.h : $(SAMHEADERS)
BamConverter.h : $(SAMHEADERS) sam_utils.h SamHeader.hpp utils.h my_assert.h bc_aux.h Transcript.h Transcripts.h
Buffer.h : my_assert.h
SamHeader.hpp : $(SAMHEADERS)
# Compile EBSeq
ebseq :
cd EBSeq && $(MAKE) all
# Compile pRSEM
pRSEM :
cd pRSEM && $(MAKE) all
# Install RSEM
install : $(PROGRAMS) $(SCRIPTS) rsem_perl_utils.pm
$(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; )
$(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;)
$(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm
# Clean
clean :
rm -f *.o *~ $(PROGRAMS)
cd EBSeq && $(MAKE) clean
cd pRSEM && $(MAKE) clean
|
