[med-svn] [rsem] 02/02: adapt to new upstream layout
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun May 15 16:34:21 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to tag debian/1.2.30+dfsg-1
in repository rsem.
commit d1e06e11a7d9d866d9cf2b2eec2dff36cae2e011
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Mon Mar 7 04:00:48 2016 -0800
adapt to new upstream layout
---
debian/changelog | 10 ++++
debian/clean | 1 +
debian/control | 9 +--
debian/copyright | 62 +++++++++++++++++++-
debian/patches/add-descriptions | 80 -------------------------
debian/patches/fix-boost | 64 --------------------
debian/patches/fix-for-g++-6 | 13 -----
debian/patches/fix-sam-includes | 126 ----------------------------------------
debian/patches/hardening | 20 +++++++
debian/patches/ignore-sam | 108 ----------------------------------
debian/patches/series | 8 +--
debian/patches/spelling | 49 ----------------
debian/patches/use-flags | 119 -------------------------------------
debian/rsem.lintian-overrides | 5 +-
debian/rules | 16 ++---
15 files changed, 108 insertions(+), 582 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 0e6df09..44b7b08 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+rsem (1.2.30+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+ * Use upstream's modified samtools-1.3 as that is required for correct
+ operation
+ * re-enable hardening to match source changes
+ * generate manual pages for rsem-bam2wig & rsem-simulate-reads
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sun, 15 May 2016 03:49:04 -0700
+
rsem (1.2.26+dfsg-3) unstable; urgency=medium
* Team upload.
diff --git a/debian/clean b/debian/clean
index 0f65186..91bba9b 100644
--- a/debian/clean
+++ b/debian/clean
@@ -1 +1,2 @@
debian/*.1
+samtools-1.3/config.mk
diff --git a/debian/control b/debian/control
index b0a14e5..2a9c947 100644
--- a/debian/control
+++ b/debian/control
@@ -1,18 +1,19 @@
Source: rsem
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>,
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
Andreas Tille <tille at debian.org>
Section: science
Priority: extra
Build-Depends: debhelper (>= 9),
zlib1g-dev,
libncurses5-dev,
- libbam-dev,
libboost-dev,
perl,
python,
- bowtie | bowtie2,
- help2man
+ help2man,
+ bowtie | bowtie2
+# bowtie is a run-time dependency available on only a few systems, not actually
+# needed for building but it prevents the creation of uninstallable packages
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rsem.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/rsem.git
diff --git a/debian/copyright b/debian/copyright
index 020b353..ec01e08 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: RSEM
Source: http://deweylab.biostat.wisc.edu/rsem/src/
-Files-Excluded: sam boost EBSeq/*.tar.gz
+Files-Excluded: boost EBSeq/*.tar.gz
Files: *
Copyright: (c) 2009-2015 Bo Li bli25 [at] berkeley [dot] edu
@@ -9,6 +9,7 @@ License: GPL-3
Files: debian/*
Copyright: (c) 2015 Michigan State University
+ (c) 2016 Michael R. Crusoe
License: GPL-3
License: GPL-3
@@ -27,3 +28,62 @@ License: GPL-3
On Debian systems, the full text of the GNU General Public
License version 3 can be found in the file
`/usr/share/common-licenses/GPL-3'.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz
+
+Files: samtools-1.3/*
+Copyright: © 2008–2016, Genome Research Ltd. (GRL)
+ © 2003–2006, 2008–2011, by Heng Li <lh3lh3 at live.co.uk>
+ © 2009–2012 Broad Institute
+ © 2010 Illumina, Inc.
+ © 2012–2013 Peter Cock, The James Hutton Institute.
+License: MIT
+Comment: Modified version of samtools included as per upstream
+
+Files: samtools-1.3/win32/xcurses.h
+Copyright: Public Domain
+License: public-domain
+ This file is part of PDCurses (http://pdcurses.sourceforge.net/),
+ which is in the public domain.
+
+Files: samtools-1.3/win32/z*.h
+Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
+License: zlib
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+ .
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+ .
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+ .
+ Jean-loup Gailly Mark Adler
+ jloup at gzip.org madler at alumni.caltech.edu
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
diff --git a/debian/patches/add-descriptions b/debian/patches/add-descriptions
deleted file mode 100644
index c6f8717..0000000
--- a/debian/patches/add-descriptions
+++ /dev/null
@@ -1,80 +0,0 @@
-Description: add whatisdb compatible descripts to Perl scripts with existing
-POD documentation
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- rsem.orig/convert-sam-for-rsem
-+++ rsem/convert-sam-for-rsem
-@@ -89,7 +89,7 @@
-
- =head1 NAME
-
--convert-sam-for-rsem
-+convert-sam-for-rsem - make a RSEM compatible BAM file
-
- =head1 SYNOPSIS
-
---- rsem.orig/rsem-calculate-expression
-+++ rsem/rsem-calculate-expression
-@@ -578,7 +578,7 @@
-
- =head1 NAME
-
--rsem-calculate-expression
-+rsem-calculate-expression - estimates gene and isoform expression from RNA-Seq data
-
- =head1 SYNOPSIS
-
---- rsem.orig/rsem-control-fdr
-+++ rsem/rsem-control-fdr
-@@ -62,7 +62,7 @@
-
- =head1 NAME
-
--rsem-control-fdr
-+rsem-control-fdr - filter ebseq output for statistical significance
-
- =head1 SYNOPSIS
-
---- rsem.orig/rsem-generate-ngvector
-+++ rsem/rsem-generate-ngvector
-@@ -33,7 +33,7 @@
-
- =head1 NAME
-
--rsem-generate-ngvector
-+rsem-generate-ngvector - create Ng vector for EBSeq for de-novo transcriptomes
-
- =head1 SYNOPSIS
-
---- rsem.orig/rsem-plot-transcript-wiggles
-+++ rsem/rsem-plot-transcript-wiggles
-@@ -77,7 +77,7 @@
-
- =head1 NAME
-
--rsem-plot-transcript-wiggles
-+rsem-plot-transcript-wiggles - PDF wiggle plots from transcript or gene ids
-
- =head1 SYNOPSIS
-
---- rsem.orig/rsem-prepare-reference
-+++ rsem/rsem-prepare-reference
-@@ -158,7 +158,7 @@
-
- =head1 NAME
-
--rsem-prepare-reference
-+rsem-prepare-reference - required preprocessor of transcripts for RSEM
-
- =head1 SYNOPSIS
-
---- rsem.orig/rsem-run-ebseq
-+++ rsem/rsem-run-ebseq
-@@ -38,7 +38,7 @@
-
- =head1 NAME
-
--rsem-run-ebseq
-+rsem-run-ebseq - wrapper for EBSeq to perform differential expression analysis
-
- =head1 SYNOPSIS
-
diff --git a/debian/patches/fix-boost b/debian/patches/fix-boost
deleted file mode 100644
index e39bbd8..0000000
--- a/debian/patches/fix-boost
+++ /dev/null
@@ -1,64 +0,0 @@
-Description: use Debian's boost library
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- rsem.orig/Makefile
-+++ rsem/Makefile
-@@ -1,6 +1,6 @@
- CC = g++
--CFLAGS = -Wall -c -I.
--COFLAGS = -Wall -O3 -ffast-math -c -I.
-+CFLAGS = -Wall -c -I. -I/usr/include/
-+COFLAGS = -Wall -O3 -ffast-math -c -I. -I/usr/include
- 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
-@@ -59,8 +59,6 @@
- $(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
-@@ -77,14 +75,12 @@
-
- BamWriter.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
- $(CC) -o rsem-run-em EM.o /usr/lib/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 simul.h sam_rsem_aux.h sampling.h boost/ra [...]
-+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 simul.h sam_rsem_aux.h sampling.h WriteRes [...]
- $(CC) $(COFLAGS) EM.cpp
-
- BamConverter.h : utils.h my_assert.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
-@@ -104,14 +100,14 @@
- 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
- $(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 : 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
- $(CC) $(COFLAGS) Gibbs.cpp
-
- Buffer.h : my_assert.h
-@@ -120,7 +116,7 @@
- $(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
- $(CC) $(COFLAGS) calcCI.cpp
-
- rsem-get-unique : getUnique.cpp
diff --git a/debian/patches/fix-for-g++-6 b/debian/patches/fix-for-g++-6
deleted file mode 100644
index 8471ec7..0000000
--- a/debian/patches/fix-for-g++-6
+++ /dev/null
@@ -1,13 +0,0 @@
-From 705099ad77f64f8d5ced8419dd066601e1cb7287 Mon Sep 17 00:00:00 2001
-From: Bo Li <bli25 at berkeley.edu>
-Date: Thu, 4 Feb 2016 09:27:03 -0800
-Subject: [PATCH] Updated Makefile to make sure the compilation works in latest
- version of GCC
---- rsem.orig/Makefile
-+++ rsem/Makefile
-@@ -1,4 +1,4 @@
--CC = g++
-+CC = g++ -std=gnu++98
- CFLAGS = -Wall -c -I. -I/usr/include/
- COFLAGS = -Wall -O3 -ffast-math -c -I. -I/usr/include
- 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
diff --git a/debian/patches/fix-sam-includes b/debian/patches/fix-sam-includes
deleted file mode 100644
index 97ddc31..0000000
--- a/debian/patches/fix-sam-includes
+++ /dev/null
@@ -1,126 +0,0 @@
-Description: correct the samtools includes to match standard paths
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- rsem.orig/BamConverter.h
-+++ rsem/BamConverter.h
-@@ -8,8 +8,8 @@
- #include<map>
-
- #include <stdint.h>
--#include "sam/bam.h"
--#include "sam/sam.h"
-+#include "samtools/bam.h"
-+#include "samtools/sam.h"
- #include "sam_rsem_aux.h"
- #include "sam_rsem_cvt.h"
-
---- rsem.orig/BamWriter.h
-+++ rsem/BamWriter.h
-@@ -10,8 +10,8 @@
- #include<iostream>
-
- #include <stdint.h>
--#include "sam/bam.h"
--#include "sam/sam.h"
-+#include "samtools/bam.h"
-+#include "samtools/sam.h"
- #include "sam_rsem_aux.h"
- #include "sam_rsem_cvt.h"
-
---- rsem.orig/SamParser.h
-+++ rsem/SamParser.h
-@@ -8,8 +8,8 @@
- #include<cassert>
- #include<string>
-
--#include "sam/bam.h"
--#include "sam/sam.h"
-+#include "samtools/bam.h"
-+#include "samtools/sam.h"
-
- #include "utils.h"
- #include "my_assert.h"
---- rsem.orig/bc_aux.h
-+++ rsem/bc_aux.h
-@@ -4,7 +4,7 @@
- #include<map>
-
- #include <stdint.h>
--#include "sam/bam.h"
-+#include "samtools/bam.h"
-
- struct SingleEndT {
- bam1_t *b;
---- rsem.orig/sam_rsem_aux.h
-+++ rsem/sam_rsem_aux.h
-@@ -5,7 +5,7 @@
- #include<cstring>
- #include<stdint.h>
-
--#include "sam/bam.h"
-+#include "samtools/bam.h"
-
- // dwt: duplicate without text
- bam_header_t *bam_header_dwt(const bam_header_t *ori_h)
---- rsem.orig/sam_rsem_cvt.h
-+++ rsem/sam_rsem_cvt.h
-@@ -4,7 +4,7 @@
- #include<vector>
-
- #include "stdint.h"
--#include "sam/bam.h"
-+#include "samtools/bam.h"
-
- #include "Transcript.h"
- #include "Transcripts.h"
---- rsem.orig/getUnique.cpp
-+++ rsem/getUnique.cpp
-@@ -6,8 +6,8 @@
- #include<vector>
-
- #include <stdint.h>
--#include "sam/bam.h"
--#include "sam/sam.h"
-+#include "samtools/bam.h"
-+#include "samtools/sam.h"
-
- #include "utils.h"
-
---- rsem.orig/samValidator.cpp
-+++ rsem/samValidator.cpp
-@@ -6,8 +6,8 @@
- #include<set>
-
- #include <stdint.h>
--#include "sam/bam.h"
--#include "sam/sam.h"
-+#include "samtools/bam.h"
-+#include "samtools/sam.h"
-
- #include "utils.h"
- #include "my_assert.h"
---- rsem.orig/scanForPairedEndReads.cpp
-+++ rsem/scanForPairedEndReads.cpp
-@@ -7,8 +7,8 @@
- #include<algorithm>
-
- #include <stdint.h>
--#include "sam/bam.h"
--#include "sam/sam.h"
-+#include "samtools/bam.h"
-+#include "samtools/sam.h"
-
- #include "utils.h"
- #include "my_assert.h"
---- rsem.orig/wiggle.cpp
-+++ rsem/wiggle.cpp
-@@ -4,8 +4,8 @@
- #include <iostream>
-
- #include <stdint.h>
--#include "sam/bam.h"
--#include "sam/sam.h"
-+#include "samtools/bam.h"
-+#include "samtools/sam.h"
-
- #include "utils.h"
- #include "wiggle.h"
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 0000000..a297f00
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,20 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: accept the hardening flags
+--- rsem.orig/Makefile
++++ rsem/Makefile
+@@ -12,11 +12,11 @@
+
+ # Compilation variables
+ CXX = g++
+-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
+-CPPFLAGS =
++CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB)
++CPPFLAGS ?=
+
+-LDFLAGS =
+-LDLIBS =
++LDFLAGS ?=
++LDLIBS ?=
+
+ # Installation variables
+ INSTALL = install
diff --git a/debian/patches/ignore-sam b/debian/patches/ignore-sam
deleted file mode 100644
index b2419ab..0000000
--- a/debian/patches/ignore-sam
+++ /dev/null
@@ -1,108 +0,0 @@
-Description: don't build local copy of samtools
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- a/Makefile
-+++ b/Makefile
-@@ -7,9 +7,6 @@
-
- all : $(PROGRAMS)
-
--sam/libbam.a :
-- cd sam ; ${MAKE} all
--
- Transcript.h : utils.h
-
- Transcripts.h : utils.h my_assert.h Transcript.h
-@@ -48,13 +45,13 @@
- 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
-+SamParser.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
-+rsem-parse-alignments : parseIt.o
-+ $(CC) -o rsem-parse-alignments parseIt.o /usr/lib/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 : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h parseIt.cpp
- $(CC) -Wall -O2 -c -I. parseIt.cpp
-
-
-@@ -76,36 +73,32 @@
-
- HitWrapper.h : HitContainer.h
-
--sam_rsem_aux.h : sam/bam.h
--
--sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
-+sam_rsem_cvt.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
-+BamWriter.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
-+rsem-run-em : EM.o
-+ $(CC) -o rsem-run-em EM.o /usr/lib/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 : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h simul.h sam_rsem_aux.h sampling.h boost/ra [...]
- $(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
-+BamConverter.h : utils.h my_assert.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
-- $(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp
-+ $(CC) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-
--rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
-- $(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o bam2wig.cpp
-+ $(CC) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-
--rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
-- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o bam2readdepth.cpp
-+ $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-
--wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
-+wiggle.o: wiggle.cpp wiggle.h
- $(CC) $(COFLAGS) wiggle.cpp
-
- rsem-simulate-reads : simulation.o
-@@ -130,19 +123,17 @@
- 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 : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
-- $(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-get-unique : getUnique.cpp
-+ $(CC) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-
--rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
-- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-sam-validator : my_assert.h samValidator.cpp
-+ $(CC) -O3 -Wall samValidator.cpp /usr/lib/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
-- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-scan-for-paired-end-reads : my_assert.h scanForPairedEndReads.cpp
-+ $(CC) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-
- ebseq :
- cd EBSeq ; ${MAKE} all
-
- clean :
- rm -f *.o *~ $(PROGRAMS)
-- cd sam ; ${MAKE} clean
-- cd EBSeq ; ${MAKE} clean
diff --git a/debian/patches/series b/debian/patches/series
index f3aad13..997a9fc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1 @@
-spelling
-ignore-sam
-fix-sam-includes
-fix-boost
-use-flags
-add-descriptions
-fix-for-g++-6
+hardening
diff --git a/debian/patches/spelling b/debian/patches/spelling
deleted file mode 100644
index 3cfe416..0000000
--- a/debian/patches/spelling
+++ /dev/null
@@ -1,49 +0,0 @@
-Author: Michael R. Crusoe
-Description: fix spelling errors
---- rsem.orig/rsem-calculate-expression
-+++ rsem/rsem-calculate-expression
-@@ -666,11 +666,11 @@
-
- =item B<--sampling-for-bam>
-
--When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
-+When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
-
- =item B<--seed> <uint32>
-
--Set the seed for the random number generators used in calculating posterior mean estimates and credibility intervals. The seed must be a non-negative 32 bit interger. (Default: off)
-+Set the seed for the random number generators used in calculating posterior mean estimates and credibility intervals. The seed must be a non-negative 32 bit integer. (Default: off)
-
- =item B<--single-cell-prior>
-
-@@ -776,7 +776,7 @@
-
- =item B<--sort-bam-by-read-name>
-
--Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce determinstic maximum likelihood estimations from independet runs. Note that sorting will take long time and lots of memory. (Default: off)
-+Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce deterministic maximum likelihood estimations from independet runs. Note that sorting will take long time and lots of memory. (Default: off)
-
- =item B<--sort-bam-buffer-size> <string>
-
---- rsem.orig/README.md
-+++ rsem/README.md
-@@ -492,7 +492,7 @@
- obtain an accurate gene-isoform relationship. Instead, RSEM provides a
- script `rsem-generate-ngvector`, which clusters transcripts based on
- measures directly relating to read mappaing ambiguity. First, it
--calcualtes the 'unmappability' of each transcript. The 'unmappability'
-+calculates the 'unmappability' of each transcript. The 'unmappability'
- of a transcript is the ratio between the number of k mers with at
- least one perfect match to other transcripts and the total number of k
- mers of this transcript, where k is a parameter. Then, Ng vector is
---- rsem.orig/rsem-generate-ngvector
-+++ rsem/rsem-generate-ngvector
-@@ -69,7 +69,7 @@
-
- =head1 DESCRIPTION
-
--This program generates the Ng vector required by EBSeq for isoform level differential expression analysis based on reference sequences only. EBSeq can take variance due to read mapping ambiguity into consideration by grouping isoforms with parent gene's number of isoforms. However, for de novo assembled transcriptome, it is hard to obtain an accurate gene-isoform relationship. Instead, this program groups isoforms by using measures on read mappaing ambiguity directly. First, it calcualt [...]
-+This program generates the Ng vector required by EBSeq for isoform level differential expression analysis based on reference sequences only. EBSeq can take variance due to read mapping ambiguity into consideration by grouping isoforms with parent gene's number of isoforms. However, for de novo assembled transcriptome, it is hard to obtain an accurate gene-isoform relationship. Instead, this program groups isoforms by using measures on read mappaing ambiguity directly. First, it calculat [...]
-
- If your reference is a de novo assembled transcript set, you should run 'rsem-generate-ngvector' first. Then load the resulting 'output_name.ngvec' into R. For example, you can use
-
diff --git a/debian/patches/use-flags b/debian/patches/use-flags
deleted file mode 100644
index 163dcd2..0000000
--- a/debian/patches/use-flags
+++ /dev/null
@@ -1,119 +0,0 @@
-Description: pass CXXFLAGS to compiler
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- a/Makefile
-+++ b/Makefile
-@@ -12,10 +12,10 @@
- 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
-- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-+ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-
- rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
-- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-+ $(CC) $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-
- BowtieRefSeqPolicy.h : RefSeqPolicy.h
-
-@@ -25,10 +25,10 @@
-
-
- rsem-preref : preRef.o
-- $(CC) preRef.o -o rsem-preref
-+ $(CC) $(CPPFLAGS) $(LDFLAGS) preRef.o -o rsem-preref
-
- preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
-- $(CC) $(COFLAGS) preRef.cpp
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(COFLAGS) preRef.cpp
-
-
- SingleRead.h : Read.h
-@@ -49,14 +49,14 @@
-
-
- rsem-parse-alignments : parseIt.o
-- $(CC) -o rsem-parse-alignments parseIt.o /usr/lib/libbam.a -lz -lpthread
-+ $(CC) $(LDFLAGS) -o rsem-parse-alignments parseIt.o /usr/lib/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 parseIt.cpp
-- $(CC) -Wall -O2 -c -I. parseIt.cpp
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) -Wall -O2 -c -I. parseIt.cpp
-
-
- rsem-build-read-index : utils.h buildReadIndex.cpp
-- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
-
-
- ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
-@@ -78,55 +78,55 @@
- 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
-- $(CC) -o rsem-run-em EM.o /usr/lib/libbam.a -lz -lpthread
-+ $(CC) $(LDFLAGS) -o rsem-run-em EM.o /usr/lib/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 simul.h sam_rsem_aux.h sampling.h WriteRes [...]
-- $(CC) $(COFLAGS) EM.cpp
-+ $(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) EM.cpp
-
- BamConverter.h : utils.h my_assert.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_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp
-- $(CC) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall tbam2gbam.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-
- rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o bam2wig.cpp
-- $(CC) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall bam2wig.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-
- rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o bam2readdepth.cpp
-- $(CC) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall bam2readdepth.cpp wiggle.o /usr/lib/libbam.a -lz -lpthread -o $@
-
- wiggle.o: wiggle.cpp wiggle.h
-- $(CC) $(COFLAGS) wiggle.cpp
-+ $(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) wiggle.cpp
-
- rsem-simulate-reads : simulation.o
-- $(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
-- $(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
-
- #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
-- $(CC) $(COFLAGS) Gibbs.cpp
-+ $(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) Gibbs.cpp
-
- Buffer.h : my_assert.h
-
- rsem-calculate-credibility-intervals : calcCI.o
-- $(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-+ $(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
-- $(CC) $(COFLAGS) calcCI.cpp
-+ $(CC) $(CPPFLAGS) $(COFLAGS) $(CXXFLAGS) calcCI.cpp
-
- rsem-get-unique : getUnique.cpp
-- $(CC) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall getUnique.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-
- rsem-sam-validator : my_assert.h samValidator.cpp
-- $(CC) -O3 -Wall samValidator.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall samValidator.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-
- rsem-scan-for-paired-end-reads : my_assert.h scanForPairedEndReads.cpp
-- $(CC) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-+ $(CC) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -O3 -Wall scanForPairedEndReads.cpp /usr/lib/libbam.a -lz -lpthread -o $@
-
- ebseq :
- cd EBSeq ; ${MAKE} all
diff --git a/debian/rsem.lintian-overrides b/debian/rsem.lintian-overrides
index b12c406..bca601a 100644
--- a/debian/rsem.lintian-overrides
+++ b/debian/rsem.lintian-overrides
@@ -1,4 +1 @@
-rsem: spelling-error-in-binary usr/bin/rsem-calculate-credibility-intervals ressize resize
-rsem: spelling-error-in-binary usr/bin/rsem-run-em ressize resize
-rsem: spelling-error-in-binary usr/bin/rsem-run-gibbs ressize resize
-rsem: spelling-error-in-binary usr/bin/rsem-simulate-reads ressize resize
+rsem: spelling-error-in-binary usr/bin/* compres compress
diff --git a/debian/rules b/debian/rules
index 3c1b96c..0523d73 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,12 +5,13 @@ DH_VERBOSE := 1
DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
dh $@ --parallel
override_dh_auto_build:
+ dh_auto_build -- BOOST=/usr/include prefix=debian/tmp
for prog in convert-sam-for-rsem rsem-calculate-expression \
rsem-control-fdr rsem-generate-ngvector \
rsem-plot-transcript-wiggles rsem-prepare-reference \
@@ -18,16 +19,17 @@ override_dh_auto_build:
help2man ./rsem-gff3-to-gtf --no-info --version-string="${VERSION}" \
--name 'Convert GFF3 files to GTF files.' > \
debian/rsem-gff3-to-gtf.1
- dh_auto_build
+ help2man ./rsem-bam2wig --no-info --version-string="${VERSION}" \
+ --name 'Convert BAM files to wiggle files.' > \
+ debian/rsem-bam2wig.1
+ help2man ./rsem-simulate-reads --no-info --version-string="${VERSION}" \
+ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \
+ debian/rsem-simulate-reads.1
override_dh_auto_install:
find . -maxdepth 1 -type f -perm /u+x | xargs -n 1 -I{} dh_install {} /usr/bin/
dh_install rsem_perl_utils.pm /usr/share/perl5
- dh_auto_install
-
-override_dh_auto_clean:
- mkdir -p sam
- dh_auto_clean
+ dh_auto_install -- BOOST=/usr/include prefix=debian/tmp
get-orig-source:
uscan --verbose --force-download --repack --compression xz
--
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