[med-svn] [rsem] 06/07: new upstream release & refresh patches
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Mar 5 12:36:10 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch 1.2.28
in repository rsem.
commit bd646787d662d5b7b9b82ae0c65fdb1c6952e72b
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Mon Feb 22 05:17:36 2016 -0800
new upstream release & refresh patches
---
debian/changelog | 2 +-
debian/patches/add-descriptions | 4 ++--
debian/patches/fix-boost | 35 +++++++++++++++++++++++------------
debian/patches/spelling | 1 +
debian/patches/use-flags | 30 +++++++++++++++++++-----------
debian/rules | 2 ++
6 files changed, 48 insertions(+), 26 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 283ee6c..964985b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-rsem (1.2.27+dfsg-1) UNRELEASED; urgency=medium
+rsem (1.2.28+dfsg-1) UNRELEASED; urgency=medium
* New upstream release
diff --git a/debian/patches/add-descriptions b/debian/patches/add-descriptions
index 2fcc797..d8224bf 100644
--- a/debian/patches/add-descriptions
+++ b/debian/patches/add-descriptions
@@ -1,6 +1,6 @@
-Description: add whatisdb compatible descripts to Perl scripts with existing
-POD documentation
+Description: add whatisdb compatible descripts to Perl scripts with existing POD documentation
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Forwarded: https://github.com/deweylab/RSEM/pull/23
--- rsem.orig/convert-sam-for-rsem
+++ rsem/convert-sam-for-rsem
@@ -56,7 +56,7 @@
diff --git a/debian/patches/fix-boost b/debian/patches/fix-boost
index 29c2a7d..fee53fa 100644
--- a/debian/patches/fix-boost
+++ b/debian/patches/fix-boost
@@ -1,38 +1,49 @@
Description: use Debian's boost library
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Forwarded: https://github.com/deweylab/RSEM/pull/22
--- rsem.orig/Makefile
+++ rsem/Makefile
-@@ -70,8 +70,6 @@
- $(CC) $(LFLAGS) buildReadIndex.cpp -o rsem-build-read-index
+@@ -7,6 +7,7 @@
+ HTSLIB = htslib-1.3
+ SAMFLAGS = -I$(SAMTOOLS) -I$(SAMTOOLS)/$(HTSLIB)
+ SAMLIBS = $(SAMTOOLS)/libbam.a $(SAMTOOLS)/$(HTSLIB)/libhts.a
++BOOST = boost # overriderable by distributions
+ 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
--simul.h : boost/random.hpp
+@@ -71,8 +72,7 @@
+ rsem-build-read-index : utils.h buildReadIndex.cpp
+ $(CC) $(LFLAGS) buildReadIndex.cpp -o rsem-build-read-index
+
-
+-simul.h : boost/random.hpp
++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
-@@ -88,14 +86,12 @@
+@@ -90,14 +90,14 @@
BamWriter.h : $(SAMTOOLS)/sam.h $(SAMTOOLS)/bam.h sam_utils.h utils.h my_assert.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
-sampling.h : boost/random.hpp
--
++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 $(SAMLIBS)
$(CC) -o rsem-run-em EM.o $(SAMLIBS) -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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
-+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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
++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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
$(CC) $(COFLAGS) $(SAMFLAGS) EM.cpp
bc_aux.h : $(SAMTOOLS)/bam.h
-@@ -118,14 +114,14 @@
+@@ -120,14 +120,14 @@
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 : 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 WriteResults.h simulation.cpp
++simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/random.hpp WriteResults.h simulation.cpp
$(CC) $(COFLAGS) simulation.cpp
rsem-run-gibbs : Gibbs.o
@@ -40,16 +51,16 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
#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 : utils.h my_assert.h 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 : utils.h my_assert.h $(BOOST)/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp
$(CC) $(COFLAGS) Gibbs.cpp
Buffer.h : my_assert.h
-@@ -134,7 +130,7 @@
+@@ -136,7 +136,7 @@
$(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 : utils.h my_assert.h 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 : utils.h my_assert.h $(BOOST)/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
$(CC) $(COFLAGS) calcCI.cpp
rsem-get-unique : $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h sam_utils.h utils.h getUnique.cpp $(SAMLIBS)
diff --git a/debian/patches/spelling b/debian/patches/spelling
index 781c6dd..0ad91bb 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,5 +1,6 @@
Author: Michael R. Crusoe
Description: fix spelling errors
+Forwarded: https://github.com/deweylab/RSEM/pull/21
--- rsem.orig/rsem-calculate-expression
+++ rsem/rsem-calculate-expression
@@ -645,7 +645,7 @@
diff --git a/debian/patches/use-flags b/debian/patches/use-flags
index cc2941f..fb6847c 100644
--- a/debian/patches/use-flags
+++ b/debian/patches/use-flags
@@ -2,7 +2,7 @@ Description: pass CXXFLAGS to compiler
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
--- rsem.orig/Makefile
+++ rsem/Makefile
-@@ -22,10 +22,10 @@
+@@ -25,10 +25,10 @@
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
@@ -15,7 +15,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
BowtieRefSeqPolicy.h : RefSeqPolicy.h
-@@ -35,10 +35,10 @@
+@@ -38,10 +38,10 @@
rsem-preref : preRef.o
@@ -28,12 +28,12 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
SingleRead.h : Read.h
-@@ -60,14 +60,14 @@
+@@ -63,14 +63,14 @@
rsem-parse-alignments : parseIt.o $(SAMLIBS)
- $(CC) -o rsem-parse-alignments parseIt.o $(SAMLIBS) -lz -lpthread
-+ $(CC) $(LDFLAGS) -o rsem-parse-alignments parseIt.o $(SAMLIBS) -lz -lpthread
++ $(CC) $(LDFLAGS) -o rsem-parse-alignments parseIt.o $(SAMLIBS) -lz -lpthread
parseIt.o : $(SAMTOOLS)/sam.h $(SAMTOOLS)/bam.h sam_utils.h utils.h my_assert.h GroupInfo.h Transcripts.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h parseIt.cpp
- $(CC) -Wall -O2 -c -I. $(SAMFLAGS) parseIt.cpp
@@ -44,16 +44,16 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
- $(CC) $(LFLAGS) buildReadIndex.cpp -o rsem-build-read-index
+ $(CC) $(LFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) buildReadIndex.cpp -o rsem-build-read-index
+ simul.h : $(BOOST)/random.hpp
- ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
-@@ -89,58 +89,58 @@
+@@ -95,64 +95,64 @@
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 $(SAMLIBS)
- $(CC) -o rsem-run-em EM.o $(SAMLIBS) -lz -lpthread
+ $(CC) $(LDFLAGS) -o rsem-run-em EM.o $(SAMLIBS) -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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
+ 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 $(SAMTOOLS)/bam.h $(SAMTOOLS)/sam.h simul. [...]
- $(CC) $(COFLAGS) $(SAMFLAGS) EM.cpp
+ $(CC) $(CPPFLAGS) $(COFLAGS) $(SAMFLAGS) $(CXXFLAGS) EM.cpp
@@ -82,16 +82,16 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
- $(CC) -o rsem-simulate-reads simulation.o
+ $(CC) $(CPPFLAGS) $(LDFLAGS) -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 WriteResults.h simulation.cpp
+ simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h $(BOOST)/random.hpp WriteResults.h simulation.cpp
- $(CC) $(COFLAGS) simulation.cpp
+ $(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) simulation.cpp
rsem-run-gibbs : Gibbs.o
- $(CC) -o rsem-run-gibbs Gibbs.o -lpthread
-+ $(CC) $(CPPFLAGS) $(LDFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
++ $(CC) $(CPPFLAGS) $(CXXFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
#some header files are omitted
- Gibbs.o : utils.h my_assert.h 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 : utils.h my_assert.h $(BOOST)/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp
- $(CC) $(COFLAGS) Gibbs.cpp
+ $(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) Gibbs.cpp
@@ -102,7 +102,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+ $(CC) $(CPPFLAGS) $(LDFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
#some header files are omitted
- calcCI.o : utils.h my_assert.h 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 : utils.h my_assert.h $(BOOST)/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
- $(CC) $(COFLAGS) calcCI.cpp
+ $(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) calcCI.cpp
@@ -120,3 +120,11 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
ebseq :
cd EBSeq ; ${MAKE} all
+
+ clean :
+ rm -f *.o *~ $(PROGRAMS)
+- cd $(SAMTOOLS) ; ${MAKE} clean
++ cd $(SAMTOOLS) && ${MAKE} clean || /bin/true
+ rm -f $(SAMLIBS)
+- cd EBSeq ; ${MAKE} clean
++ cd EBSeq && ${MAKE} clean || /bin/true
diff --git a/debian/rules b/debian/rules
index 260056c..5b22a35 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,6 +6,8 @@ DEB_TARGET_MULTIARCH=$(shell dpkg-architecture -qDEB_TARGET_MULTIARCH)
DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+export BOOST=/usr/include/boost
+
%:
dh $@ --parallel
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rsem.git
More information about the debian-med-commit
mailing list