gnu: Add rsem.
* gnu/packages/bioinformatics.scm (rsem): New variable. * gnu/packages/patches/rsem-makefile.patch: New file.master
Ricardo Wurmus
parent
21461f27e7
commit
66e3eff1e3
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@ -1013,6 +1013,84 @@ files and writing bioinformatics applications.")
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generated using the PacBio Iso-Seq protocol.")
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(license license:bsd-3))))
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(define-public rsem
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(package
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(name "rsem")
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(version "1.2.20")
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(source
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(origin
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(method url-fetch)
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(uri
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(string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
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version ".tar.gz"))
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(sha256
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(base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
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(patches (list (search-patch "rsem-makefile.patch")))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; remove bundled copy of boost
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(delete-file-recursively "boost")
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#t))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no "check" target
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#:phases
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(modify-phases %standard-phases
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;; No "configure" script.
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;; Do not build bundled samtools library.
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(replace 'configure
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(lambda _
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(substitute* "Makefile"
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(("^all : sam/libbam.a") "all : "))
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#t))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (string-append (assoc-ref outputs "out")))
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(bin (string-append out "/bin/"))
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(perl (string-append out "/lib/perl5/site_perl")))
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(mkdir-p bin)
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(mkdir-p perl)
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(for-each (lambda (file)
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(copy-file file
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(string-append bin (basename file))))
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(find-files "." "rsem-.*"))
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(copy-file "rsem_perl_utils.pm"
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(string-append perl "/rsem_perl_utils.pm")))
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#t))
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(add-after
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'install 'wrap-program
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(for-each (lambda (prog)
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(wrap-program (string-append out "/bin/" prog)
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`("PERL5LIB" ":" prefix
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(,(string-append out "/lib/perl5/site_perl")))))
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'("rsem-plot-transcript-wiggles"
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"rsem-calculate-expression"
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"rsem-generate-ngvector"
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"rsem-run-ebseq"
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"rsem-prepare-reference")))
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#t)))))
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(inputs
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`(("boost" ,boost)
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("ncurses" ,ncurses)
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("r" ,r)
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("perl" ,perl)
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("samtools" ,samtools-0.1)
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("zlib" ,zlib)))
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(home-page "http://deweylab.biostat.wisc.edu/rsem/")
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(synopsis "Estimate gene expression levels from RNA-Seq data")
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(description
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"RSEM is a software package for estimating gene and isoform expression
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levels from RNA-Seq data. The RSEM package provides a user-friendly
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interface, supports threads for parallel computation of the EM algorithm,
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single-end and paired-end read data, quality scores, variable-length reads and
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RSPD estimation. In addition, it provides posterior mean and 95% credibility
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interval estimates for expression levels. For visualization, it can generate
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BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
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(license license:gpl3+)))
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(define-public rseqc
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(package
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(name "rseqc")
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@ -0,0 +1,682 @@
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This patch simplifies the Makefile, making it much easier to build rsem
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without the bundled version of samtools. It has already been submitted
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upstream: https://github.com/bli25wisc/RSEM/pull/11
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From 161894e91a16c7e15af57e4fcfe8cb613711c7fa Mon Sep 17 00:00:00 2001
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From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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Date: Wed, 22 Apr 2015 14:51:07 +0200
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Subject: [PATCH 1/7] remove all headers from Makefile
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---
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Makefile | 95 +++++++++++-----------------------------------------------------
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1 file changed, 16 insertions(+), 79 deletions(-)
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diff --git a/Makefile b/Makefile
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index 54e2603..3a55ed8 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -10,133 +10,70 @@ all : $(PROGRAMS)
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sam/libbam.a :
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cd sam ; ${MAKE} all
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-Transcript.h : utils.h
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-
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-Transcripts.h : utils.h my_assert.h Transcript.h
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-
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-rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
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+rsem-extract-reference-transcripts : extractRef.cpp
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$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
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-rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
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+rsem-synthesis-reference-transcripts : synthesisRef.cpp
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$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
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-BowtieRefSeqPolicy.h : RefSeqPolicy.h
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-
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-RefSeq.h : utils.h
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-
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-Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
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-
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-
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rsem-preref : preRef.o
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$(CC) preRef.o -o rsem-preref
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-preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
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+preRef.o : preRef.cpp
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$(CC) $(COFLAGS) preRef.cpp
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-
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-SingleRead.h : Read.h
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-
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-SingleReadQ.h : Read.h
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-
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-PairedEndRead.h : Read.h SingleRead.h
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-
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-PairedEndReadQ.h : Read.h SingleReadQ.h
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-
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-
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-PairedEndHit.h : SingleHit.h
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-
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-HitContainer.h : GroupInfo.h
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-
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-
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-SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
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-
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-
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rsem-parse-alignments : parseIt.o sam/libbam.a
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$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
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-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
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+parseIt.o : parseIt.cpp
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$(CC) -Wall -O2 -c -I. parseIt.cpp
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-
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-rsem-build-read-index : utils.h buildReadIndex.cpp
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+rsem-build-read-index : buildReadIndex.cpp
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$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
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-
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-simul.h : boost/random.hpp
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-
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-ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
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-
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-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
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-
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-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
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-
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-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
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-
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-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
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-
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-HitWrapper.h : HitContainer.h
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-
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-sam_rsem_aux.h : sam/bam.h
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-
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-sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
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-
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-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
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-
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-sampling.h : boost/random.hpp
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-
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-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
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-
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rsem-run-em : EM.o sam/libbam.a
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$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
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-EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
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+EM.o : EM.cpp
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$(CC) $(COFLAGS) EM.cpp
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-bc_aux.h : sam/bam.h
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-
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-BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
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-
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-rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
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+rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
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$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
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-rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
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+rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
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$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
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-rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
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+rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
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$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
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-wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
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+wiggle.o: wiggle.cpp
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$(CC) $(COFLAGS) wiggle.cpp
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rsem-simulate-reads : simulation.o
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$(CC) -o rsem-simulate-reads simulation.o
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-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
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+simulation.o : simulation.cpp
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$(CC) $(COFLAGS) simulation.cpp
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rsem-run-gibbs : Gibbs.o
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$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
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-#some header files are omitted
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-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
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+Gibbs.o : Gibbs.cpp
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$(CC) $(COFLAGS) Gibbs.cpp
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-Buffer.h : my_assert.h
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-
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rsem-calculate-credibility-intervals : calcCI.o
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$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
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-#some header files are omitted
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-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
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+calcCI.o : calcCI.cpp
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$(CC) $(COFLAGS) calcCI.cpp
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-rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
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+rsem-get-unique : getUnique.cpp sam/libbam.a
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$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
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-rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
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+rsem-sam-validator : samValidator.cpp sam/libbam.a
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$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
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-rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
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+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
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$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
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ebseq :
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From ec136638a727632e20abfaeb65c22c46d15ca8c4 Mon Sep 17 00:00:00 2001
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From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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Date: Wed, 22 Apr 2015 15:06:41 +0200
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Subject: [PATCH 2/7] include current dir, ./sam and ./boost by default
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---
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Makefile | 48 ++++++++++++++++++++++++------------------------
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1 file changed, 24 insertions(+), 24 deletions(-)
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diff --git a/Makefile b/Makefile
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index 3a55ed8..1dd97ca 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -1,6 +1,6 @@
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CC = g++
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-CFLAGS = -Wall -c -I.
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-COFLAGS = -Wall -O3 -ffast-math -c -I.
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+CFLAGS = -Wall -I. -I./sam -I./boost
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+COFLAGS = -O3 -ffast-math -c
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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
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.PHONY : all ebseq clean
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@@ -11,70 +11,70 @@ sam/libbam.a :
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cd sam ; ${MAKE} all
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rsem-extract-reference-transcripts : extractRef.cpp
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- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
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+ $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
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rsem-synthesis-reference-transcripts : synthesisRef.cpp
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- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
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+ $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
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rsem-preref : preRef.o
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- $(CC) preRef.o -o rsem-preref
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+ $(CC) $(CFLAGS) preRef.o -o rsem-preref
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preRef.o : preRef.cpp
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- $(CC) $(COFLAGS) preRef.cpp
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+ $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
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rsem-parse-alignments : parseIt.o sam/libbam.a
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- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
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+ $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
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parseIt.o : parseIt.cpp
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- $(CC) -Wall -O2 -c -I. parseIt.cpp
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+ $(CC) $(CFLAGS) -O2 -c parseIt.cpp
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rsem-build-read-index : buildReadIndex.cpp
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- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
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+ $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
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rsem-run-em : EM.o sam/libbam.a
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- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
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+ $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
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EM.o : EM.cpp
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- $(CC) $(COFLAGS) EM.cpp
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+ $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
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rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
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- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
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+ $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
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rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
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- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
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+ $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
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rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
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- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
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+ $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
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wiggle.o: wiggle.cpp
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- $(CC) $(COFLAGS) wiggle.cpp
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+ $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
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rsem-simulate-reads : simulation.o
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- $(CC) -o rsem-simulate-reads simulation.o
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+ $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
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simulation.o : simulation.cpp
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- $(CC) $(COFLAGS) simulation.cpp
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+ $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
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rsem-run-gibbs : Gibbs.o
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- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
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+ $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
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Gibbs.o : Gibbs.cpp
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- $(CC) $(COFLAGS) Gibbs.cpp
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+ $(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
|
||||
|
||||
Loading…
Reference in New Issue