debian/0000775000000000000000000000000012234053713007170 5ustar debian/upstream0000664000000000000000000000104312234051027010745 0ustar Contact: Cole Trapnell Homepage: http://tophat.cbcb.umd.edu/ Name: TopHat Reference: author: Cole Trapnell and Lior Pachter and Steven L. Salzberg title: > TopHat: discovering splice junctions with RNA-Seq journal: Bioinformatics volume: 25 number: 9 pages: 1105-1111 year: 2009 DOI: 10.1093/bioinformatics/btp120 PMID: 19289445 URL: http://bioinformatics.oxfordjournals.org/content/25/9/1105.short eprint: http://bioinformatics.oxfordjournals.org/content/25/9/1105.full.pdf+html license: Open Access debian/source/0000775000000000000000000000000012234051027010464 5ustar debian/source/format0000664000000000000000000000001412234051027011672 0ustar 3.0 (quilt) debian/copyright0000664000000000000000000001234712234051031011121 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: TopHat Upstream-Contact: Cole Trapnell Source: http://tophat.cbcb.umd.edu/downloads/tophat-2.0.9.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 for SOLiD reads. The SeqAn-1.2 library is used in TopHat and Bowtie and some of its sources are included in TopHat source releases; its authors are Andreas Doring, David Weese, Tobias Rausch, and Knut Reinert. Files: * Copyright: © 2003-2010 Cole Trapnell et al License: Artistic Files: ax_bam.m4 Copyright: © 2010 Cole Trapnell License: GAP Files: ax_boost_thread.m4 Copyright: © 2009 Thomas Porschberg © 2009 Michael Tindal License: GAP Files: ax_boost_base.m4 Copyright: © 2009 Thomas Porschberg License: GAP Files: build-aux/* Copyright: © 1994-2005 Free Software Foundation, Inc. License: GPL-2+ with Autoconf exception This file is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program 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 General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. . As a special exception to the GNU General Public License, if you distribute this file as part of a program that contains a configuration script generated by Autoconf, you may include it under the same distribution terms that you use for the rest of that program. Files: build-aux/install-sh Copyright: © 1994 X Consortium License: 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 X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. . Except as contained in this notice, the name of the X Consortium shall not be used in advertising or otherwise to promote the sale, use or other deal- ings in this Software without prior written authorization from the X Consor- tium. Comment: FSF changes to this file are in the public domain. Files: aclocal.m4 Copyright: © 1996-2005 Free Software Foundation, Inc. License: This file is free software; the Free Software Foundation gives unlimited permission to copy and/or distribute it, with or without modifications, as long as this notice is preserved. Files: INSTALL configure Copyright: © 1992-2010 Free Software Foundation, Inc. License: This configure script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it. Files: debian/* Copyright: © 2011 Carlos Borroto © 2013 Alex Mestiashvili License: GPL-2+ License: GAP Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. License: Artistic This program is free software; you can redistribute it and/or modify it under the terms of the Artistic License, which comes with Perl. . On Debian systems, the complete text of the Artistic License can be found in `/usr/share/common-licenses/Artistic'. License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package 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 General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/changelog0000664000000000000000000001314412234053174011046 0ustar tophat (2.0.9-1ubuntu1) trusty; urgency=low * Merge from Debian, remaining changes: - Link against boost system. * Specify multiarch boost libdir location. -- Dmitrijs Ledkovs Wed, 30 Oct 2013 00:26:37 +0000 tophat (2.0.9-1) unstable; urgency=low * d/get-orig-source: place tarballs to ../tarballs/ * d/control: use canonical vcs fields, Standards-Version: 3.9.4 * d/changelog: updated source field * refreshed patches * Imported Upstream version 2.0.9 -- Alexandre Mestiashvili Thu, 04 Jul 2013 13:59:07 +0200 tophat (2.0.8b-1ubuntu1) saucy; urgency=low * Link against boost system. -- Dmitrijs Ledkovs Tue, 28 May 2013 13:51:28 +0100 tophat (2.0.8b-1) unstable; urgency=low * Imported Upstream version 2.0.8b Closes: #707059 -- Alexandre Mestiashvili Tue, 07 May 2013 22:58:36 +0200 tophat (2.0.8-1) unstable; urgency=low * Imported Upstream version 2.0.8 -- Alexandre Mestiashvili Sat, 02 Mar 2013 12:38:32 +0100 tophat (2.0.7-1) unstable; urgency=low * Imported Upstream version 2.0.7 -- Alexandre Mestiashvili Sat, 23 Feb 2013 11:45:36 +0100 tophat (2.0.6-1) unstable; urgency=low * Team upload [ Carlos Borroto ] * Imported Upstream version 2.0.6 -- Charles Plessy Tue, 06 Nov 2012 14:54:31 +0900 tophat (2.0.5-1) unstable; urgency=low [ Alexandre Mestiashvili ] * Imported Upstream version 2.0.5 -- Alexandre Mestiashvili Fri, 05 Oct 2012 10:56:26 +0200 tophat (2.0.3-1) unstable; urgency=low * Imported Upstream version 2.0.3 -- Alexandre Mestiashvili Sat, 09 Jun 2012 11:06:21 +0200 tophat (2.0.0-2) unstable; urgency=low * debian/upstream: BibTeX conform author syntax * debian/patces/bashism_in_shell_script.patch: Fix bashism in shell script Closes: #671813 * debhelper 9 (control+compat) * debian/rules: Create some manpages using help2man -- Andreas Tille Sun, 06 May 2012 13:26:38 +0200 tophat (2.0.0-1) unstable; urgency=low [ Charles Plessy ] * YAML syntax correction [ 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 * debian/get-orig-source - removes shipped with tophat SeqAn files. -- Alexandre Mestiashvili Sat, 14 Apr 2012 12:47:32 +0200 tophat (1.4.1-2) unstable; urgency=low [ Carlos Borroto ] * added bowtie as a binary dependency * suggests cufflinks [ Andreas Tille ] * debian/control: Added myself to uploaders * debian/patches/remove_cflag_handling_in_configure.patch: Enable better support for different architectures (Thanks to Peter Michael Green for the patch) Closes: #660309 * debian/upstream: Added references -- Andreas Tille Sat, 18 Feb 2012 08:22:50 +0100 tophat (1.4.1-1) unstable; urgency=low * Team upload. * Initial upload to Debian archive. [ Carlos Borroto ] * New upstream release [ Charles Plessy ] * Corrected VCS URL. * Minor description changes. * Recommend bowtie. * debian/copyright: - Normalised with config-edit --application dpkg-copyright. - Documented SeqAn and m4 macros. * Merged patches bam2samtools and fix_includes_path.patch (same purpose). * Build-depend only on python. * Tighten build-dependancy on sequan-dev. -- Charles Plessy Mon, 06 Feb 2012 16:12:29 +0900 tophat (1.4.0-1) UNRELEASED; urgency=low * New upstream release - debian/patches/fix_undefined_reference.patch -- Carlos Borroto Tue, 10 Jan 2012 11:49:39 -0500 tophat (1.3.3-1) UNRELEASED; urgency=low TODO: * src/SeqAn-1.2 should be excluded - tophat depends on seqan library which already exists in debian [Alexandre Mestiashvili] * New upstream release * Removed dh-make template from watch file * Added initial copyright data , removed templates , added Source * debian/compat version 8 * debian/control - Maintainer: Debian Med Packaging Team - DM-Upload-Allowed: yes - Added myself to Uploaders: - added correct Vcs-Git , Vcs-Browser fields - Standards-Version: 3.9.2 - added build-dependency quilt - added seqan-dev as dependency * debian/rules - removed dh-make template * debian/control Added python dependency to binary package * debian/control Description shouldn't start with package name * debian/rules removed quilt patch management * Added DEP3 headers to patches. * Added Pre-Depends: dpkg (>= 1.15.6) (xz compression) Fixed syntax-error in debian/copyright -- Alexandre Mestiashvili Thu, 05 Jan 2012 14:37:19 +0100 tophat (1.3.1-1ppa1~lucid1) lucid; urgency=low * New upstream version -- Carlos Borroto Thu, 23 Jun 2011 11:02:22 -0400 tophat (1.3.0-1ppa1~lucid1) lucid; urgency=low * Backported to lucid -- Carlos Borroto Wed, 08 Jun 2011 14:56:32 -0400 tophat (1.3.0-1) UNRELEASED; urgency=low * Initial release * debian/patches/fix_includes_path.patch * debian/patches/fix-configure.patch -- Carlos Borroto Wed, 08 Jun 2011 14:34:56 -0400 debian/control0000664000000000000000000000257612234051314010600 0ustar Source: tophat Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Carlos Borroto , Alexandre Mestiashvili , Andreas Tille Build-Depends: debhelper (>= 9), autotools-dev, libbam-dev (>=0.1.16), zlib1g-dev, dh-autoreconf, python (>=2.6.6-3~), seqan-dev (>= 1.3~), libboost-thread-dev, libboost-system-dev, help2man Standards-Version: 3.9.4 Homepage: http://tophat.cbcb.umd.edu/ Vcs-Git: git://anonscm.debian.org/debian-med/tophat.git Vcs-Browser: http://anonscm.debian.org/gitweb/?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~), bowtie2 | bowtie 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 mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology. debian/rules0000775000000000000000000000204612234052707010254 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 include /usr/share/dpkg/default.mk pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- ) mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1 bindir=$(CURDIR)/debian/$(pkg)/usr/bin %: dh $@ --with autoreconf override_dh_builddeb: dh_builddeb -- -Z xz override_dh_auto_configure: dh_auto_configure -- --with-boost-libdir=/usr/lib/$(DEB_HOST_MULTIARCH) override_dh_auto_install: dh_auto_install # try to create man pages whereever possible mkdir -p $(mandir) help2man --no-info --no-discard-stderr -h "" \ --name='converts bam directly into fastx' \ --version-string="$(version)" \ $(bindir)/bam2fastx > $(mandir)/bam2fastx.1 help2man --no-info --no-discard-stderr \ --name='TopHat maps short sequences from spliced transcripts to whole genomes' \ --version-string="$(version)" \ $(bindir)/tophat > $(mandir)/tophat.1 debian/watch0000664000000000000000000000011512234051027010212 0ustar version=3 http://tophat.cbcb.umd.edu/downloads/tophat-([-0-9.]*\w?)\.tar\.gz debian/get-orig-source0000775000000000000000000000125012234051027012123 0ustar #!/bin/sh # script to download and repack source package of tophat # stripping off SeqAn which is distributed in Debian. PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` mkdir -p ../tarballs VERSION=`uscan --verbose --force-download --destdir='../tarballs/' | \ grep "Newest version on remote site is .* local version is .*" | \ head -n 1 | \ sed "s/Newest version on remote site is \([-0-9.].*\),.*/\1/"` cd ../tarballs UPSTREAMNAME=tophat UPSTREAMDIR="${UPSTREAMNAME}-${VERSION}" tar -xzf ${UPSTREAMDIR}.tar.gz rm -rf ${UPSTREAMDIR}/src/SeqAn-1.3 GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}" rm -rf "${UPSTREAMDIR}" debian/patches/0000775000000000000000000000000012234051031010606 5ustar debian/patches/bashism_in_shell_script.patch0000664000000000000000000000065012234051031016517 0ustar Author: Andreas Tille Bug-Closed: http://bugs.debian.org/671813 Descriptions: Remove bashism from shell script --- a/src/tophat2.in +++ b/src/tophat2.in @@ -1,9 +1,9 @@ #!/bin/bash prefix="__PREFIX__" pbin="" -if [[ -z $prefix ]]; then +if [ "$prefix" = "" ]; then fl=$(readlink $0) - if [[ -z $fl ]]; then + if [ "$fl" = "" ]; then pbin=$(dirname $0) else pbin=$(dirname $fl) debian/patches/fix_includes_path.patch0000664000000000000000000000271612234051031015325 0ustar From: Alexandre Mestiashvili Date: 2012-01-05 Subject: Corrected location for samtools .h files --- a/src/align_status.h +++ b/src/align_status.h @@ -14,7 +14,7 @@ #include #include #include -#include +#include #include "common.h" #include "bwt_map.h" --- a/src/bam2fastx.cpp +++ b/src/bam2fastx.cpp @@ -5,8 +5,8 @@ #include #include -#include "bam/bam.h" -#include "bam/sam.h" +#include "samtools/bam.h" +#include "samtools/sam.h" using namespace std; --- a/src/bwt_map.h +++ b/src/bwt_map.h @@ -16,7 +16,7 @@ #include #include -#include +#include using namespace std; #include "common.h" --- a/src/common.h +++ b/src/common.h @@ -15,8 +15,8 @@ #include #include #include -#include "bam/bam.h" -#include "bam/sam.h" +#include "samtools/bam.h" +#include "samtools/sam.h" #define MAX_READ_LEN 1024 --- a/src/map2gtf.h +++ b/src/map2gtf.h @@ -20,8 +20,8 @@ #include #include -#include -#include +#include +#include #include --- a/ax_bam.m4 +++ b/ax_bam.m4 @@ -102,7 +102,7 @@ AC_LANG_PUSH(C++) AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ - @%:@include + @%:@include ]], [[ ]])],[ AC_MSG_RESULT(yes) debian/patches/boost-link-system.patch0000664000000000000000000000355212234051027015244 0ustar Description: in a crude way link boost_system Author: Dmitrijs Ledkovs --- tophat-2.0.6.orig/ax_boost_thread.m4 +++ tophat-2.0.6/ax_boost_thread.m4 @@ -60,7 +60,7 @@ AC_DEFUN([AX_BOOST_THREAD], export CPPFLAGS LDFLAGS_SAVED="$LDFLAGS" - LDFLAGS="$LDFLAGS $BOOST_LDFLAGS" + LDFLAGS="$LDFLAGS $BOOST_LDFLAGS -lboost_system" export LDFLAGS AC_CACHE_CHECK(whether the Boost::Thread library is available, @@ -107,14 +107,14 @@ AC_DEFUN([AX_BOOST_THREAD], for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do ax_lib=${libextension} AC_CHECK_LIB($ax_lib, exit, - [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], [link_thread="no"]) done if test "x$link_thread" != "xyes"; then for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do ax_lib=${libextension} AC_CHECK_LIB($ax_lib, exit, - [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], + [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break], [link_thread="no"]) done fi debian/patches/series0000664000000000000000000000011612234051027012026 0ustar fix_includes_path.patch bashism_in_shell_script.patch boost-link-system.patch debian/docs0000664000000000000000000000001412234051027010032 0ustar NEWS README debian/compat0000664000000000000000000000000212234051027010362 0ustar 9