[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-14-g1ebd078
Alexandre Mestiashvili
alex at biotec.tu-dresden.de
Sat Apr 14 10:11:03 UTC 2012
The following commit has been merged in the master branch:
commit 1ebd0789996a9eb1d9c576039ad2a433522058bb
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Sat Apr 14 11:52:34 2012 +0200
debian/control Standards-Version: 3.9.3 Depends: bowtie2
debian/copyright updated Format, removed seqan copyright statements
debian/patches removed unneeded patches
diff --git a/debian/changelog b/debian/changelog
index 7bf50c6..35e385d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,8 +6,13 @@ tophat (2.0.0-1) UNRELEASED; urgency=low
[ Alexandre Mestiashvili ]
* Imported Upstream version 2.0.0
* updated debian/patches
+ * debian/control added libboost-thread-dev dependency,
+ added bowtie2 to Suggests:
+ * debian/control Standards-Version: 3.9.3 Depends: bowtie2
+ * debian/copyright updated Format, removed seqan copyright statements
+ * debian/patches removed unneeded patches
- -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Sat, 14 Apr 2012 10:47:13 +0200
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Sat, 14 Apr 2012 11:56:48 +0200
tophat (1.4.1-2) unstable; urgency=low
diff --git a/debian/control b/debian/control
index 3d8f4c8..808019d 100644
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,7 @@ Uploaders: Carlos Borroto <carlos.borroto at gmail.com>,
Build-Depends: debhelper (>= 8), autotools-dev, libbam-dev (>=0.1.16),
zlib1g-dev, dh-autoreconf, python (>=2.6.6-3~), seqan-dev (>= 1.3~),
libboost-thread-dev
-Standards-Version: 3.9.2
+Standards-Version: 3.9.3
Homepage: http://tophat.cbcb.umd.edu/
Vcs-Git: git://git.debian.org/debian-med/tophat.git
Vcs-Browser: http://git.debian.org/?p=debian-med/tophat.git
@@ -17,8 +17,8 @@ Vcs-Browser: http://git.debian.org/?p=debian-med/tophat.git
Package: tophat
Architecture: any
Pre-Depends: dpkg (>= 1.15.6~)
-Depends: ${shlibs:Depends}, ${misc:Depends}, python (>=2.6.6-3~), bowtie
-Suggests: cufflinks, bowtie2
+Depends: ${shlibs:Depends}, ${misc:Depends}, python (>=2.6.6-3~), bowtie2
+Suggests: cufflinks, bowtie
Description: fast splice junction mapper for RNA-Seq reads
TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra
high-throughput short read aligner Bowtie, and then analyzes the
diff --git a/debian/copyright b/debian/copyright
index 841e870..eaf706f 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
-Format: http://dep.debian.net/deps/dep5
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: TopHat
Upstream-Contact: Cole Trapnell <cole at cs.umd.edu>
-Source: http://tophat.cbcb.umd.edu/downloads/tophat-1.4.1.tar.gz
+Source: http://tophat.cbcb.umd.edu/downloads/tophat-2.0.0.tar.gz
Comment:
Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by
Ben Langmead and Cole Trapnell. Daehwan Kim and Geo Pertea added support
@@ -13,37 +13,6 @@ Files: *
Copyright: © 2003-2010 Cole Trapnell et al
License: Artistic
-Files: src/SeqAn-1.2/*
-Upstream-Name: SeqAn
-Copyright: © 2007
-License: LGPL-3+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 3 of the License, or (at your option) any later version.
- .
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
- .
- On Debian systems, the complete text of the GNU Lesser General Public License
- version 3 can be found in the files ‘/usr/share/common-licenses/LGPL-3’ and
- ‘/usr/share/common-licenses/GPL-3’.
-
-Files: src/SeqAn-1.2/index_sa_lss.h
-Copyright: © 1999, N. Jesper Larsson, all rights reserved.
-License: qsufsort.c
- This file contains an implementation of the algorithm presented in "Faster
- Suffix Sorting" by N. Jesper Larsson (jesper at cs.lth.se) and Kunihiko
- Sadakane (sada at is.s.u-tokyo.ac.jp).
- .
- This software may be used freely for any purpose. However, when distributed,
- the original source must be clearly stated, and, when the source code is
- distributed, the copyright notice must be retained and any alterations in
- the code must be clearly marked. No warranty is given regarding the quality
- of this software.
-
Files: ax_bam.m4
Copyright: © 2010 Cole Trapnell <cole at cs.umd.edu>
License: GAP
diff --git a/debian/patches/debian_seqan.patch b/debian/patches/debian_seqan.patch
deleted file mode 100644
index e308bf5..0000000
--- a/debian/patches/debian_seqan.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
-Date: 2012-01-05
-Subject: Adopted to use with seqan v1.3. Function reverseInPlace renamed to
-reverse and convertInPlace to convert
---- tophat.orig/configure.ac
-+++ tophat/configure.ac
-@@ -117,7 +117,7 @@
- CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
- CXXFLAGS="$CFLAGS $BAM_CPPFLAGS"
-
--AM_CXXFLAGS="$CXXFLAGS -I./SeqAn-1.2"
-+AM_CXXFLAGS="$CXXFLAGS -I/usr/include/seqan"
-
- AC_SUBST(CC)
- AC_SUBST(AM_CXXFLAGS)
---- tophat.orig/src/segment_juncs.cpp
-+++ tophat/src/segment_juncs.cpp
-@@ -2670,12 +2670,12 @@
- if(color){
- fullRead = read.seq.c_str() + 1;
- rcRead = fullRead;
-- seqan::reverseInPlace(rcRead);
-+ seqan::reverse(rcRead);
- }else{
- fullRead = read.seq;
- rcRead = read.seq;
-- seqan::convertInPlace(rcRead, seqan::FunctorComplement<Dna>());
-- seqan::reverseInPlace(rcRead);
-+ seqan::convert(rcRead, seqan::FunctorComplement<Dna>());
-+ seqan::reverse(rcRead);
- }
-
- size_t read_length = seqan::length(fullRead);
-@@ -2878,8 +2878,8 @@
- seqan::String<char> fullRead, rcRead;
- fullRead = read.seq;
- rcRead = read.seq;
-- seqan::convertInPlace(rcRead, seqan::FunctorComplement<Dna>());
-- seqan::reverseInPlace(rcRead);
-+ seqan::convert(rcRead, seqan::FunctorComplement<Dna>());
-+ seqan::reverse(rcRead);
- size_t read_length = read.seq.length();
-
- for (size_t l = 0; l < left_segment_hits.hits.size(); ++l)
diff --git a/debian/patches/remove_cflag_handling_in_configure.patch b/debian/patches/remove_cflag_handling_in_configure.patch
deleted file mode 100644
index 5d1ed78..0000000
--- a/debian/patches/remove_cflag_handling_in_configure.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Description: Remove crazy cflag determination code
- This code was broken (for example the test for -m64 plain doesn't work)
- and does the wrong thing (uses -m686 on x86) for debian. Strip it out
- completely
-Author: Peter Michael Green <plugwash at p10link.net>
-Origin: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-February/014089.html
-Bug-Debian: http://bugs.debian.org/660309
-Forwarded: no
-Reviewed-By: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 18 Feb 2012 03:37:47 +0000
-
---- tophat-1.4.1.orig/configure.ac
-+++ tophat-1.4.1/configure.ac
-@@ -75,26 +75,6 @@ generic_CFLAGS="-Wall -Wno-strict-aliasi
- ext_CFLAGS=""
- debug_CFLAGS="-g"
- #echo "${host_cpu}-${host_os}"
--case "${host_cpu}-${host_os}" in
-- i*86-*linux*)
-- ext_CFLAGS="-march=i686";;
-- i*86-darwin*)
-- AC_ARG_ENABLE(universal, [ --enable-universal enable universal binary (Intel Apple only)],
-- [is_uni=1], [is_uni=0])
-- case $is_uni in
-- 1) CFLAGS="-m64"
-- AC_COMPILE_IFELSE([AC_LANG_PROGRAM],
-- [ext_CFLAGS="-arch x86_64 -arch i386 -arch ppc64 -arch ppc"],
-- [ext_CFLAGS="-arch i386 -arch ppc"]);;
-- 0) CFLAGS="-m64"
-- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
-- esac;;
-- *)
-- AC_MSG_CHECKING([if gcc accepts -m64])
-- CFLAGS="-m64"
-- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])],
-- [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);;
--esac
-
- AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2],
- [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
--
A spliced read mapper for RNA-Seq
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