mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2025-01-12 14:16:55 -05:00
gnu: rsem: Update to 1.3.1.
* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1. [source]: Fetch from git; remove patch; delete bundled samtools. [arguments]: Pass make flags; adjust phases. [inputs]: Remove ncurses and samtools-0.1; add htslib-1.3. * gnu/packages/patches/rsem-makefile.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it.
This commit is contained in:
Ricardo Wurmus
Ricardo Wurmus
parent
a235ea4f30
commit
89ee8a6edf
3 changed files with 52 additions and 722 deletions
|
|
@ -1115,7 +1115,6 @@ dist_patch_DATA = \
|
||||||
%D%/packages/patches/reptyr-fix-gcc-7.patch \
|
%D%/packages/patches/reptyr-fix-gcc-7.patch \
|
||||||
%D%/packages/patches/ripperx-missing-file.patch \
|
%D%/packages/patches/ripperx-missing-file.patch \
|
||||||
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
|
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
|
||||||
%D%/packages/patches/rsem-makefile.patch \
|
|
||||||
%D%/packages/patches/rtags-separate-rct.patch \
|
%D%/packages/patches/rtags-separate-rct.patch \
|
||||||
%D%/packages/patches/racket-store-checksum-override.patch \
|
%D%/packages/patches/racket-store-checksum-override.patch \
|
||||||
%D%/packages/patches/ruby-rubygems-276-for-ruby24.patch \
|
%D%/packages/patches/ruby-rubygems-276-for-ruby24.patch \
|
||||||
|
|
|
||||||
|
|
@ -4800,66 +4800,79 @@ (define-public raxml
|
||||||
(define-public rsem
|
(define-public rsem
|
||||||
(package
|
(package
|
||||||
(name "rsem")
|
(name "rsem")
|
||||||
(version "1.2.20")
|
(version "1.3.1")
|
||||||
(source
|
(source
|
||||||
(origin
|
(origin
|
||||||
(method url-fetch)
|
(method git-fetch)
|
||||||
(uri
|
(uri (git-reference
|
||||||
(string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
|
(url "https://github.com/deweylab/RSEM.git")
|
||||||
version ".tar.gz"))
|
(commit (string-append "v" version))))
|
||||||
(sha256
|
(sha256
|
||||||
(base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
|
(base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
|
||||||
(patches (search-patches "rsem-makefile.patch"))
|
(file-name (git-file-name name version))
|
||||||
(modules '((guix build utils)))
|
(modules '((guix build utils)))
|
||||||
(snippet
|
(snippet
|
||||||
'(begin
|
'(begin
|
||||||
;; remove bundled copy of boost
|
;; remove bundled copy of boost and samtools
|
||||||
(delete-file-recursively "boost")
|
(delete-file-recursively "boost")
|
||||||
|
(delete-file-recursively "samtools-1.3")
|
||||||
#t))))
|
#t))))
|
||||||
(build-system gnu-build-system)
|
(build-system gnu-build-system)
|
||||||
(arguments
|
(arguments
|
||||||
`(#:tests? #f ;no "check" target
|
`(#:tests? #f ;no "check" target
|
||||||
|
#:make-flags
|
||||||
|
(list (string-append "BOOST="
|
||||||
|
(assoc-ref %build-inputs "boost")
|
||||||
|
"/include/")
|
||||||
|
(string-append "SAMHEADERS="
|
||||||
|
(assoc-ref %build-inputs "htslib")
|
||||||
|
"/include/htslib/sam.h")
|
||||||
|
(string-append "SAMLIBS="
|
||||||
|
(assoc-ref %build-inputs "htslib")
|
||||||
|
"/lib/libhts.a"))
|
||||||
#:phases
|
#:phases
|
||||||
(modify-phases %standard-phases
|
(modify-phases %standard-phases
|
||||||
;; No "configure" script.
|
;; No "configure" script.
|
||||||
;; Do not build bundled samtools library.
|
;; Do not build bundled samtools library.
|
||||||
(replace 'configure
|
(replace 'configure
|
||||||
(lambda _
|
(lambda _
|
||||||
(substitute* "Makefile"
|
(substitute* "Makefile"
|
||||||
(("^all : sam/libbam.a") "all : "))
|
(("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
|
||||||
#t))
|
(("^\\$\\(SAMLIBS\\).*") ""))
|
||||||
|
#t))
|
||||||
(replace 'install
|
(replace 'install
|
||||||
(lambda* (#:key outputs #:allow-other-keys)
|
(lambda* (#:key outputs #:allow-other-keys)
|
||||||
(let* ((out (string-append (assoc-ref outputs "out")))
|
(let* ((out (string-append (assoc-ref outputs "out")))
|
||||||
(bin (string-append out "/bin/"))
|
(bin (string-append out "/bin/"))
|
||||||
(perl (string-append out "/lib/perl5/site_perl")))
|
(perl (string-append out "/lib/perl5/site_perl")))
|
||||||
(mkdir-p bin)
|
(mkdir-p bin)
|
||||||
(mkdir-p perl)
|
(mkdir-p perl)
|
||||||
(for-each (lambda (file)
|
(for-each (lambda (file)
|
||||||
(install-file file bin))
|
(install-file file bin))
|
||||||
(find-files "." "rsem-.*"))
|
(find-files "." "rsem-.*"))
|
||||||
(install-file "rsem_perl_utils.pm" perl))
|
(install-file "rsem_perl_utils.pm" perl))
|
||||||
#t))
|
#t))
|
||||||
(add-after
|
(add-after 'install 'wrap-program
|
||||||
'install 'wrap-program
|
(lambda* (#:key outputs #:allow-other-keys)
|
||||||
(lambda* (#:key outputs #:allow-other-keys)
|
(let ((out (assoc-ref outputs "out")))
|
||||||
(let ((out (assoc-ref outputs "out")))
|
(for-each (lambda (prog)
|
||||||
(for-each (lambda (prog)
|
(wrap-program (string-append out "/bin/" prog)
|
||||||
(wrap-program (string-append out "/bin/" prog)
|
`("PERL5LIB" ":" prefix
|
||||||
`("PERL5LIB" ":" prefix
|
(,(string-append out "/lib/perl5/site_perl")))))
|
||||||
(,(string-append out "/lib/perl5/site_perl")))))
|
'("rsem-calculate-expression"
|
||||||
'("rsem-plot-transcript-wiggles"
|
"rsem-control-fdr"
|
||||||
"rsem-calculate-expression"
|
"rsem-generate-data-matrix"
|
||||||
"rsem-generate-ngvector"
|
"rsem-generate-ngvector"
|
||||||
"rsem-run-ebseq"
|
"rsem-plot-transcript-wiggles"
|
||||||
"rsem-prepare-reference")))
|
"rsem-prepare-reference"
|
||||||
#t)))))
|
"rsem-run-ebseq"
|
||||||
|
"rsem-run-prsem-testing-procedure")))
|
||||||
|
#t)))))
|
||||||
(inputs
|
(inputs
|
||||||
`(("boost" ,boost)
|
`(("boost" ,boost)
|
||||||
("ncurses" ,ncurses)
|
|
||||||
("r-minimal" ,r-minimal)
|
("r-minimal" ,r-minimal)
|
||||||
("perl" ,perl)
|
("perl" ,perl)
|
||||||
("samtools" ,samtools-0.1)
|
("htslib" ,htslib-1.3)
|
||||||
("zlib" ,zlib)))
|
("zlib" ,zlib)))
|
||||||
(home-page "http://deweylab.biostat.wisc.edu/rsem/")
|
(home-page "http://deweylab.biostat.wisc.edu/rsem/")
|
||||||
(synopsis "Estimate gene expression levels from RNA-Seq data")
|
(synopsis "Estimate gene expression levels from RNA-Seq data")
|
||||||
|
|
|
||||||
|
|
@ -1,682 +0,0 @@
|
||||||
This patch simplifies the Makefile, making it much easier to build rsem
|
|
||||||
without the bundled version of samtools. It has already been submitted
|
|
||||||
upstream: https://github.com/bli25wisc/RSEM/pull/11
|
|
||||||
|
|
||||||
From 161894e91a16c7e15af57e4fcfe8cb613711c7fa Mon Sep 17 00:00:00 2001
|
|
||||||
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
|
|
||||||
Date: Wed, 22 Apr 2015 14:51:07 +0200
|
|
||||||
Subject: [PATCH 1/7] remove all headers from Makefile
|
|
||||||
|
|
||||||
---
|
|
||||||
Makefile | 95 +++++++++++-----------------------------------------------------
|
|
||||||
1 file changed, 16 insertions(+), 79 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/Makefile b/Makefile
|
|
||||||
index 54e2603..3a55ed8 100644
|
|
||||||
--- a/Makefile
|
|
||||||
+++ b/Makefile
|
|
||||||
@@ -10,133 +10,70 @@ all : $(PROGRAMS)
|
|
||||||
sam/libbam.a :
|
|
||||||
cd sam ; ${MAKE} all
|
|
||||||
|
|
||||||
-Transcript.h : utils.h
|
|
||||||
-
|
|
||||||
-Transcripts.h : utils.h my_assert.h Transcript.h
|
|
||||||
-
|
|
||||||
-rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
|
|
||||||
+rsem-extract-reference-transcripts : extractRef.cpp
|
|
||||||
$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
|
|
||||||
|
|
||||||
-rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
|
|
||||||
+rsem-synthesis-reference-transcripts : synthesisRef.cpp
|
|
||||||
$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
|
|
||||||
|
|
||||||
-BowtieRefSeqPolicy.h : RefSeqPolicy.h
|
|
||||||
-
|
|
||||||
-RefSeq.h : utils.h
|
|
||||||
-
|
|
||||||
-Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
|
|
||||||
-
|
|
||||||
-
|
|
||||||
rsem-preref : preRef.o
|
|
||||||
$(CC) preRef.o -o rsem-preref
|
|
||||||
|
|
||||||
-preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
|
|
||||||
+preRef.o : preRef.cpp
|
|
||||||
$(CC) $(COFLAGS) preRef.cpp
|
|
||||||
|
|
||||||
-
|
|
||||||
-SingleRead.h : Read.h
|
|
||||||
-
|
|
||||||
-SingleReadQ.h : Read.h
|
|
||||||
-
|
|
||||||
-PairedEndRead.h : Read.h SingleRead.h
|
|
||||||
-
|
|
||||||
-PairedEndReadQ.h : Read.h SingleReadQ.h
|
|
||||||
-
|
|
||||||
-
|
|
||||||
-PairedEndHit.h : SingleHit.h
|
|
||||||
-
|
|
||||||
-HitContainer.h : GroupInfo.h
|
|
||||||
-
|
|
||||||
-
|
|
||||||
-SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
|
|
||||||
-
|
|
||||||
-
|
|
||||||
rsem-parse-alignments : parseIt.o sam/libbam.a
|
|
||||||
$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
|
|
||||||
|
|
||||||
-parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
|
|
||||||
+parseIt.o : parseIt.cpp
|
|
||||||
$(CC) -Wall -O2 -c -I. parseIt.cpp
|
|
||||||
|
|
||||||
-
|
|
||||||
-rsem-build-read-index : utils.h buildReadIndex.cpp
|
|
||||||
+rsem-build-read-index : buildReadIndex.cpp
|
|
||||||
$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
|
|
||||||
|
|
||||||
-
|
|
||||||
-simul.h : boost/random.hpp
|
|
||||||
-
|
|
||||||
-ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
|
|
||||||
-
|
|
||||||
-SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
|
|
||||||
-
|
|
||||||
-SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h
|
|
||||||
-
|
|
||||||
-PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h
|
|
||||||
-
|
|
||||||
-PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h
|
|
||||||
-
|
|
||||||
-HitWrapper.h : HitContainer.h
|
|
||||||
-
|
|
||||||
-sam_rsem_aux.h : sam/bam.h
|
|
||||||
-
|
|
||||||
-sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
|
|
||||||
-
|
|
||||||
-BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
|
|
||||||
-
|
|
||||||
-sampling.h : boost/random.hpp
|
|
||||||
-
|
|
||||||
-WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h
|
|
||||||
-
|
|
||||||
rsem-run-em : EM.o sam/libbam.a
|
|
||||||
$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
|
|
||||||
|
|
||||||
-EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
|
|
||||||
+EM.o : EM.cpp
|
|
||||||
$(CC) $(COFLAGS) EM.cpp
|
|
||||||
|
|
||||||
-bc_aux.h : sam/bam.h
|
|
||||||
-
|
|
||||||
-BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
|
|
||||||
-
|
|
||||||
-rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
|
|
||||||
+rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
|
|
||||||
$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
|
|
||||||
+rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
|
|
||||||
$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
|
|
||||||
+rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
|
|
||||||
$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
|
|
||||||
+wiggle.o: wiggle.cpp
|
|
||||||
$(CC) $(COFLAGS) wiggle.cpp
|
|
||||||
|
|
||||||
rsem-simulate-reads : simulation.o
|
|
||||||
$(CC) -o rsem-simulate-reads simulation.o
|
|
||||||
|
|
||||||
-simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp
|
|
||||||
+simulation.o : simulation.cpp
|
|
||||||
$(CC) $(COFLAGS) simulation.cpp
|
|
||||||
|
|
||||||
rsem-run-gibbs : Gibbs.o
|
|
||||||
$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
|
|
||||||
|
|
||||||
-#some header files are omitted
|
|
||||||
-Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp
|
|
||||||
+Gibbs.o : Gibbs.cpp
|
|
||||||
$(CC) $(COFLAGS) Gibbs.cpp
|
|
||||||
|
|
||||||
-Buffer.h : my_assert.h
|
|
||||||
-
|
|
||||||
rsem-calculate-credibility-intervals : calcCI.o
|
|
||||||
$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
|
|
||||||
|
|
||||||
-#some header files are omitted
|
|
||||||
-calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
|
|
||||||
+calcCI.o : calcCI.cpp
|
|
||||||
$(CC) $(COFLAGS) calcCI.cpp
|
|
||||||
|
|
||||||
-rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
|
|
||||||
+rsem-get-unique : getUnique.cpp sam/libbam.a
|
|
||||||
$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
|
|
||||||
+rsem-sam-validator : samValidator.cpp sam/libbam.a
|
|
||||||
$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
|
|
||||||
+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
|
|
||||||
$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
ebseq :
|
|
||||||
|
|
||||||
From ec136638a727632e20abfaeb65c22c46d15ca8c4 Mon Sep 17 00:00:00 2001
|
|
||||||
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
|
|
||||||
Date: Wed, 22 Apr 2015 15:06:41 +0200
|
|
||||||
Subject: [PATCH 2/7] include current dir, ./sam and ./boost by default
|
|
||||||
|
|
||||||
---
|
|
||||||
Makefile | 48 ++++++++++++++++++++++++------------------------
|
|
||||||
1 file changed, 24 insertions(+), 24 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/Makefile b/Makefile
|
|
||||||
index 3a55ed8..1dd97ca 100644
|
|
||||||
--- a/Makefile
|
|
||||||
+++ b/Makefile
|
|
||||||
@@ -1,6 +1,6 @@
|
|
||||||
CC = g++
|
|
||||||
-CFLAGS = -Wall -c -I.
|
|
||||||
-COFLAGS = -Wall -O3 -ffast-math -c -I.
|
|
||||||
+CFLAGS = -Wall -I. -I./sam -I./boost
|
|
||||||
+COFLAGS = -O3 -ffast-math -c
|
|
||||||
PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
|
|
||||||
|
|
||||||
.PHONY : all ebseq clean
|
|
||||||
@@ -11,70 +11,70 @@ sam/libbam.a :
|
|
||||||
cd sam ; ${MAKE} all
|
|
||||||
|
|
||||||
rsem-extract-reference-transcripts : extractRef.cpp
|
|
||||||
- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
|
|
||||||
+ $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
|
|
||||||
|
|
||||||
rsem-synthesis-reference-transcripts : synthesisRef.cpp
|
|
||||||
- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
|
|
||||||
+ $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
|
|
||||||
|
|
||||||
rsem-preref : preRef.o
|
|
||||||
- $(CC) preRef.o -o rsem-preref
|
|
||||||
+ $(CC) $(CFLAGS) preRef.o -o rsem-preref
|
|
||||||
|
|
||||||
preRef.o : preRef.cpp
|
|
||||||
- $(CC) $(COFLAGS) preRef.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
|
|
||||||
|
|
||||||
rsem-parse-alignments : parseIt.o sam/libbam.a
|
|
||||||
- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
|
|
||||||
|
|
||||||
parseIt.o : parseIt.cpp
|
|
||||||
- $(CC) -Wall -O2 -c -I. parseIt.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O2 -c parseIt.cpp
|
|
||||||
|
|
||||||
rsem-build-read-index : buildReadIndex.cpp
|
|
||||||
- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
|
|
||||||
+ $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
|
|
||||||
|
|
||||||
rsem-run-em : EM.o sam/libbam.a
|
|
||||||
- $(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
|
|
||||||
|
|
||||||
EM.o : EM.cpp
|
|
||||||
- $(CC) $(COFLAGS) EM.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
|
|
||||||
|
|
||||||
rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
|
|
||||||
- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
|
|
||||||
- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
|
|
||||||
- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
wiggle.o: wiggle.cpp
|
|
||||||
- $(CC) $(COFLAGS) wiggle.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
|
|
||||||
|
|
||||||
rsem-simulate-reads : simulation.o
|
|
||||||
- $(CC) -o rsem-simulate-reads simulation.o
|
|
||||||
+ $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
|
|
||||||
|
|
||||||
simulation.o : simulation.cpp
|
|
||||||
- $(CC) $(COFLAGS) simulation.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
|
|
||||||
|
|
||||||
rsem-run-gibbs : Gibbs.o
|
|
||||||
- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
|
|
||||||
|
|
||||||
Gibbs.o : Gibbs.cpp
|
|
||||||
- $(CC) $(COFLAGS) Gibbs.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
|
|
||||||
|
|
||||||
rsem-calculate-credibility-intervals : calcCI.o
|
|
||||||
- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
|
|
||||||
|
|
||||||
calcCI.o : calcCI.cpp
|
|
||||||
- $(CC) $(COFLAGS) calcCI.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
|
|
||||||
|
|
||||||
rsem-get-unique : getUnique.cpp sam/libbam.a
|
|
||||||
- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-sam-validator : samValidator.cpp sam/libbam.a
|
|
||||||
- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
|
|
||||||
- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
ebseq :
|
|
||||||
cd EBSeq ; ${MAKE} all
|
|
||||||
|
|
||||||
From d366614ea50f79fdd93e3c76383ccb6fcdeaa8e0 Mon Sep 17 00:00:00 2001
|
|
||||||
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
|
|
||||||
Date: Wed, 22 Apr 2015 15:10:49 +0200
|
|
||||||
Subject: [PATCH 3/7] separate object rules from rules for executables
|
|
||||||
|
|
||||||
---
|
|
||||||
Makefile | 50 ++++++++++++++++++++++++++------------------------
|
|
||||||
1 file changed, 26 insertions(+), 24 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/Makefile b/Makefile
|
|
||||||
index 1dd97ca..ae4de3b 100644
|
|
||||||
--- a/Makefile
|
|
||||||
+++ b/Makefile
|
|
||||||
@@ -10,6 +10,32 @@ all : $(PROGRAMS)
|
|
||||||
sam/libbam.a :
|
|
||||||
cd sam ; ${MAKE} all
|
|
||||||
|
|
||||||
+ebseq :
|
|
||||||
+ cd EBSeq ; ${MAKE} all
|
|
||||||
+
|
|
||||||
+
|
|
||||||
+calcCI.o : calcCI.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
|
|
||||||
+
|
|
||||||
+EM.o : EM.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
|
|
||||||
+
|
|
||||||
+Gibbs.o : Gibbs.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
|
|
||||||
+
|
|
||||||
+preRef.o : preRef.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
|
|
||||||
+
|
|
||||||
+parseIt.o : parseIt.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O2 -c parseIt.cpp
|
|
||||||
+
|
|
||||||
+simulation.o : simulation.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
|
|
||||||
+
|
|
||||||
+wiggle.o: wiggle.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
|
|
||||||
+
|
|
||||||
+
|
|
||||||
rsem-extract-reference-transcripts : extractRef.cpp
|
|
||||||
$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
|
|
||||||
|
|
||||||
@@ -19,24 +45,15 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
|
|
||||||
rsem-preref : preRef.o
|
|
||||||
$(CC) $(CFLAGS) preRef.o -o rsem-preref
|
|
||||||
|
|
||||||
-preRef.o : preRef.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
|
|
||||||
-
|
|
||||||
rsem-parse-alignments : parseIt.o sam/libbam.a
|
|
||||||
$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
|
|
||||||
|
|
||||||
-parseIt.o : parseIt.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O2 -c parseIt.cpp
|
|
||||||
-
|
|
||||||
rsem-build-read-index : buildReadIndex.cpp
|
|
||||||
$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
|
|
||||||
|
|
||||||
rsem-run-em : EM.o sam/libbam.a
|
|
||||||
$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
|
|
||||||
|
|
||||||
-EM.o : EM.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
|
|
||||||
-
|
|
||||||
rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
|
|
||||||
$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
@@ -46,27 +63,15 @@ rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
|
|
||||||
rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
|
|
||||||
$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-wiggle.o: wiggle.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
|
|
||||||
-
|
|
||||||
rsem-simulate-reads : simulation.o
|
|
||||||
$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
|
|
||||||
|
|
||||||
-simulation.o : simulation.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
|
|
||||||
-
|
|
||||||
rsem-run-gibbs : Gibbs.o
|
|
||||||
$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
|
|
||||||
|
|
||||||
-Gibbs.o : Gibbs.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
|
|
||||||
-
|
|
||||||
rsem-calculate-credibility-intervals : calcCI.o
|
|
||||||
$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
|
|
||||||
|
|
||||||
-calcCI.o : calcCI.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
|
|
||||||
-
|
|
||||||
rsem-get-unique : getUnique.cpp sam/libbam.a
|
|
||||||
$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
@@ -76,9 +81,6 @@ rsem-sam-validator : samValidator.cpp sam/libbam.a
|
|
||||||
rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
|
|
||||||
$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-ebseq :
|
|
||||||
- cd EBSeq ; ${MAKE} all
|
|
||||||
-
|
|
||||||
clean :
|
|
||||||
rm -f *.o *~ $(PROGRAMS)
|
|
||||||
cd sam ; ${MAKE} clean
|
|
||||||
|
|
||||||
From 6ba1c33cccdf7c8e7df7a3189e7db204be3b1e8d Mon Sep 17 00:00:00 2001
|
|
||||||
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
|
|
||||||
Date: Wed, 22 Apr 2015 15:28:30 +0200
|
|
||||||
Subject: [PATCH 4/7] add ./sam to library directories, link with -lbam
|
|
||||||
|
|
||||||
---
|
|
||||||
Makefile | 36 ++++++++++++++++++------------------
|
|
||||||
1 file changed, 18 insertions(+), 18 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/Makefile b/Makefile
|
|
||||||
index ae4de3b..a87cc4d 100644
|
|
||||||
--- a/Makefile
|
|
||||||
+++ b/Makefile
|
|
||||||
@@ -1,11 +1,11 @@
|
|
||||||
CC = g++
|
|
||||||
-CFLAGS = -Wall -I. -I./sam -I./boost
|
|
||||||
+CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
|
|
||||||
COFLAGS = -O3 -ffast-math -c
|
|
||||||
PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
|
|
||||||
|
|
||||||
.PHONY : all ebseq clean
|
|
||||||
|
|
||||||
-all : $(PROGRAMS)
|
|
||||||
+all : sam/libbam.a $(PROGRAMS)
|
|
||||||
|
|
||||||
sam/libbam.a :
|
|
||||||
cd sam ; ${MAKE} all
|
|
||||||
@@ -45,23 +45,23 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
|
|
||||||
rsem-preref : preRef.o
|
|
||||||
$(CC) $(CFLAGS) preRef.o -o rsem-preref
|
|
||||||
|
|
||||||
-rsem-parse-alignments : parseIt.o sam/libbam.a
|
|
||||||
- $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
|
|
||||||
+rsem-parse-alignments : parseIt.o
|
|
||||||
+ $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
|
|
||||||
|
|
||||||
rsem-build-read-index : buildReadIndex.cpp
|
|
||||||
$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
|
|
||||||
|
|
||||||
-rsem-run-em : EM.o sam/libbam.a
|
|
||||||
- $(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
|
|
||||||
+rsem-run-em : EM.o
|
|
||||||
+ $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
|
|
||||||
|
|
||||||
-rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
|
|
||||||
- $(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+rsem-tbam2gbam : tbam2gbam.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+rsem-bam2wig : wiggle.o bam2wig.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-simulate-reads : simulation.o
|
|
||||||
$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
|
|
||||||
@@ -72,14 +72,14 @@ rsem-run-gibbs : Gibbs.o
|
|
||||||
rsem-calculate-credibility-intervals : calcCI.o
|
|
||||||
$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
|
|
||||||
|
|
||||||
-rsem-get-unique : getUnique.cpp sam/libbam.a
|
|
||||||
- $(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+rsem-get-unique : getUnique.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-sam-validator : samValidator.cpp sam/libbam.a
|
|
||||||
- $(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+rsem-sam-validator : samValidator.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
-rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
|
|
||||||
- $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
|
|
||||||
+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
clean :
|
|
||||||
rm -f *.o *~ $(PROGRAMS)
|
|
||||||
|
|
||||||
From 5402b88c269df79ee245c1c59e15f3c8282a0220 Mon Sep 17 00:00:00 2001
|
|
||||||
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
|
|
||||||
Date: Wed, 22 Apr 2015 15:33:02 +0200
|
|
||||||
Subject: [PATCH 5/7] do not repeat target name, use $@ instead
|
|
||||||
|
|
||||||
---
|
|
||||||
Makefile | 18 +++++++++---------
|
|
||||||
1 file changed, 9 insertions(+), 9 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/Makefile b/Makefile
|
|
||||||
index a87cc4d..7ec90a3 100644
|
|
||||||
--- a/Makefile
|
|
||||||
+++ b/Makefile
|
|
||||||
@@ -37,22 +37,22 @@ wiggle.o: wiggle.cpp
|
|
||||||
|
|
||||||
|
|
||||||
rsem-extract-reference-transcripts : extractRef.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
|
|
||||||
+ $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
|
|
||||||
|
|
||||||
rsem-synthesis-reference-transcripts : synthesisRef.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
|
|
||||||
+ $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
|
|
||||||
|
|
||||||
rsem-preref : preRef.o
|
|
||||||
- $(CC) $(CFLAGS) preRef.o -o rsem-preref
|
|
||||||
+ $(CC) $(CFLAGS) preRef.o -o $@
|
|
||||||
|
|
||||||
rsem-parse-alignments : parseIt.o
|
|
||||||
- $(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
|
|
||||||
|
|
||||||
rsem-build-read-index : buildReadIndex.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
|
|
||||||
+ $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
|
|
||||||
|
|
||||||
rsem-run-em : EM.o
|
|
||||||
- $(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
|
|
||||||
|
|
||||||
rsem-tbam2gbam : tbam2gbam.cpp
|
|
||||||
$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
|
|
||||||
@@ -64,13 +64,13 @@ rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
|
|
||||||
$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-simulate-reads : simulation.o
|
|
||||||
- $(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ simulation.o
|
|
||||||
|
|
||||||
rsem-run-gibbs : Gibbs.o
|
|
||||||
- $(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
|
|
||||||
|
|
||||||
rsem-calculate-credibility-intervals : calcCI.o
|
|
||||||
- $(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
|
|
||||||
|
|
||||||
rsem-get-unique : getUnique.cpp
|
|
||||||
$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
From f60784bc7aa303cc825bd87dd3f5d7d26c51bded Mon Sep 17 00:00:00 2001
|
|
||||||
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
|
|
||||||
Date: Wed, 22 Apr 2015 15:44:53 +0200
|
|
||||||
Subject: [PATCH 6/7] use automatic variables to refer to prerequisites
|
|
||||||
|
|
||||||
---
|
|
||||||
Makefile | 44 ++++++++++++++++++++++----------------------
|
|
||||||
1 file changed, 22 insertions(+), 22 deletions(-)
|
|
||||||
|
|
||||||
diff --git a/Makefile b/Makefile
|
|
||||||
index 7ec90a3..6540d81 100644
|
|
||||||
--- a/Makefile
|
|
||||||
+++ b/Makefile
|
|
||||||
@@ -15,71 +15,71 @@ ebseq :
|
|
||||||
|
|
||||||
|
|
||||||
calcCI.o : calcCI.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) $<
|
|
||||||
|
|
||||||
EM.o : EM.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) EM.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) $<
|
|
||||||
|
|
||||||
Gibbs.o : Gibbs.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) $<
|
|
||||||
|
|
||||||
preRef.o : preRef.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) $<
|
|
||||||
|
|
||||||
parseIt.o : parseIt.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O2 -c parseIt.cpp
|
|
||||||
+ $(CC) $(CFLAGS) -O2 -c $<
|
|
||||||
|
|
||||||
simulation.o : simulation.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) $<
|
|
||||||
|
|
||||||
wiggle.o: wiggle.cpp
|
|
||||||
- $(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
|
|
||||||
+ $(CC) $(CFLAGS) $(COFLAGS) $<
|
|
||||||
|
|
||||||
|
|
||||||
rsem-extract-reference-transcripts : extractRef.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $< -o $@
|
|
||||||
|
|
||||||
rsem-synthesis-reference-transcripts : synthesisRef.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $< -o $@
|
|
||||||
|
|
||||||
rsem-preref : preRef.o
|
|
||||||
- $(CC) $(CFLAGS) preRef.o -o $@
|
|
||||||
+ $(CC) $(CFLAGS) $< -o $@
|
|
||||||
|
|
||||||
rsem-parse-alignments : parseIt.o
|
|
||||||
- $(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
|
|
||||||
|
|
||||||
rsem-build-read-index : buildReadIndex.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $< -o $@
|
|
||||||
|
|
||||||
rsem-run-em : EM.o
|
|
||||||
- $(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
|
|
||||||
|
|
||||||
rsem-tbam2gbam : tbam2gbam.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-bam2wig : wiggle.o bam2wig.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-simulate-reads : simulation.o
|
|
||||||
- $(CC) $(CFLAGS) -o $@ simulation.o
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ $<
|
|
||||||
|
|
||||||
rsem-run-gibbs : Gibbs.o
|
|
||||||
- $(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ $< -lpthread
|
|
||||||
|
|
||||||
rsem-calculate-credibility-intervals : calcCI.o
|
|
||||||
- $(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
|
|
||||||
+ $(CC) $(CFLAGS) -o $@ $< -lpthread
|
|
||||||
|
|
||||||
rsem-get-unique : getUnique.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-sam-validator : samValidator.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
|
|
||||||
- $(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
|
|
||||||
+ $(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
|
|
||||||
|
|
||||||
clean :
|
|
||||||
rm -f *.o *~ $(PROGRAMS)
|
|
||||||
|
|
||||||
From 0cf9721077f67fb4ca15fdc59cbfbf24a944debd Mon Sep 17 00:00:00 2001
|
|
||||||
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
|
|
||||||
Date: Wed, 22 Apr 2015 15:49:19 +0200
|
|
||||||
Subject: [PATCH 7/7] split long line
|
|
||||||
|
|
||||||
---
|
|
||||||
Makefile | 17 ++++++++++++++++-
|
|
||||||
1 file changed, 16 insertions(+), 1 deletion(-)
|
|
||||||
|
|
||||||
diff --git a/Makefile b/Makefile
|
|
||||||
index 6540d81..0ab04a5 100644
|
|
||||||
--- a/Makefile
|
|
||||||
+++ b/Makefile
|
|
||||||
@@ -1,7 +1,22 @@
|
|
||||||
CC = g++
|
|
||||||
CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
|
|
||||||
COFLAGS = -O3 -ffast-math -c
|
|
||||||
-PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
|
|
||||||
+PROGRAMS = \
|
|
||||||
+ rsem-extract-reference-transcripts \
|
|
||||||
+ rsem-synthesis-reference-transcripts \
|
|
||||||
+ rsem-preref \
|
|
||||||
+ rsem-parse-alignments \
|
|
||||||
+ rsem-build-read-index \
|
|
||||||
+ rsem-run-em \
|
|
||||||
+ rsem-tbam2gbam \
|
|
||||||
+ rsem-run-gibbs \
|
|
||||||
+ rsem-calculate-credibility-intervals \
|
|
||||||
+ rsem-simulate-reads \
|
|
||||||
+ rsem-bam2wig \
|
|
||||||
+ rsem-get-unique \
|
|
||||||
+ rsem-bam2readdepth \
|
|
||||||
+ rsem-sam-validator \
|
|
||||||
+ rsem-scan-for-paired-end-reads
|
|
||||||
|
|
||||||
.PHONY : all ebseq clean
|
|
||||||
|
|
||||||
Loading…
Reference in a new issue