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01/01: gnu: rsem: Update to 1.3.1.
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From: |
Ricardo Wurmus |
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Subject: |
01/01: gnu: rsem: Update to 1.3.1. |
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Date: |
Thu, 20 Sep 2018 11:55:52 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit 89ee8a6edf7ceae66ff86e88778e07e80aa119fd
Author: Ricardo Wurmus <address@hidden>
Date: Thu Sep 20 17:46:34 2018 +0200
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.
---
gnu/local.mk | 1 -
gnu/packages/bioinformatics.scm | 91 +++--
gnu/packages/patches/rsem-makefile.patch | 682 -------------------------------
3 files changed, 52 insertions(+), 722 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 0ead43a..4bca986 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1115,7 +1115,6 @@ dist_patch_DATA =
\
%D%/packages/patches/reptyr-fix-gcc-7.patch \
%D%/packages/patches/ripperx-missing-file.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/racket-store-checksum-override.patch \
%D%/packages/patches/ruby-rubygems-276-for-ruby24.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67f24a6..10330cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4800,66 +4800,79 @@ phylogenies.")
(define-public rsem
(package
(name "rsem")
- (version "1.2.20")
+ (version "1.3.1")
(source
(origin
- (method url-fetch)
- (uri
- (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-";
- version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/deweylab/RSEM.git";)
+ (commit (string-append "v" version))))
(sha256
- (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
- (patches (search-patches "rsem-makefile.patch"))
+ (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
+ (file-name (git-file-name name version))
(modules '((guix build utils)))
(snippet
'(begin
- ;; remove bundled copy of boost
+ ;; remove bundled copy of boost and samtools
(delete-file-recursively "boost")
+ (delete-file-recursively "samtools-1.3")
#t))))
(build-system gnu-build-system)
(arguments
`(#: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
(modify-phases %standard-phases
;; No "configure" script.
;; Do not build bundled samtools library.
(replace 'configure
- (lambda _
- (substitute* "Makefile"
- (("^all : sam/libbam.a") "all : "))
- #t))
+ (lambda _
+ (substitute* "Makefile"
+ (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
+ (("^\\$\\(SAMLIBS\\).*") ""))
+ #t))
(replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (string-append (assoc-ref outputs "out")))
- (bin (string-append out "/bin/"))
- (perl (string-append out "/lib/perl5/site_perl")))
- (mkdir-p bin)
- (mkdir-p perl)
- (for-each (lambda (file)
- (install-file file bin))
- (find-files "." "rsem-.*"))
- (install-file "rsem_perl_utils.pm" perl))
- #t))
- (add-after
- 'install 'wrap-program
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (for-each (lambda (prog)
- (wrap-program (string-append out "/bin/" prog)
- `("PERL5LIB" ":" prefix
- (,(string-append out "/lib/perl5/site_perl")))))
- '("rsem-plot-transcript-wiggles"
- "rsem-calculate-expression"
- "rsem-generate-ngvector"
- "rsem-run-ebseq"
- "rsem-prepare-reference")))
- #t)))))
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (string-append (assoc-ref outputs "out")))
+ (bin (string-append out "/bin/"))
+ (perl (string-append out "/lib/perl5/site_perl")))
+ (mkdir-p bin)
+ (mkdir-p perl)
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "." "rsem-.*"))
+ (install-file "rsem_perl_utils.pm" perl))
+ #t))
+ (add-after 'install 'wrap-program
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (for-each (lambda (prog)
+ (wrap-program (string-append out "/bin/" prog)
+ `("PERL5LIB" ":" prefix
+ (,(string-append out "/lib/perl5/site_perl")))))
+ '("rsem-calculate-expression"
+ "rsem-control-fdr"
+ "rsem-generate-data-matrix"
+ "rsem-generate-ngvector"
+ "rsem-plot-transcript-wiggles"
+ "rsem-prepare-reference"
+ "rsem-run-ebseq"
+ "rsem-run-prsem-testing-procedure")))
+ #t)))))
(inputs
`(("boost" ,boost)
- ("ncurses" ,ncurses)
("r-minimal" ,r-minimal)
("perl" ,perl)
- ("samtools" ,samtools-0.1)
+ ("htslib" ,htslib-1.3)
("zlib" ,zlib)))
(home-page "http://deweylab.biostat.wisc.edu/rsem/";)
(synopsis "Estimate gene expression levels from RNA-Seq data")
diff --git a/gnu/packages/patches/rsem-makefile.patch
b/gnu/packages/patches/rsem-makefile.patch
deleted file mode 100644
index 5481dc6..0000000
--- a/gnu/packages/patches/rsem-makefile.patch
+++ /dev/null
@@ -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 <address@hidden>
-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 [...]
-+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 <address@hidden>
-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 <address@hidden>
-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 <address@hidden>
-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 <address@hidden>
-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 <address@hidden>
-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 <address@hidden>
-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
-