debian/0000755000000000000000000000000012162316033007163 5ustar debian/watch0000644000000000000000000000016612162316033010217 0ustar version=3 opts=filenamemangle=s/(.*)(-source)(\..*$)/$1$3/\ http://sf.net/bowtie-bio/bowtie2-([\d\.]+)\-source\.zip debian/bowtie2.install0000644000000000000000000000013212162316033012122 0ustar bowtie2 usr/bin bowtie2-align usr/bin bowtie2-build usr/bin bowtie2-inspect usr/bin debian/changelog0000644000000000000000000000764212162316033011046 0ustar bowtie2 (2.1.0-2) unstable; urgency=low * Closes: #713000 * d/control: fixed description for bowtie2-examples, bumped Standards-Version, removed DM-Upload-Allowed, use canonical vcs * d/tests/: underscore are not allowed for tests -- Alexandre Mestiashvili Tue, 25 Jun 2013 13:58:18 +0200 bowtie2 (2.1.0-1) unstable; urgency=low * - d/help2man-wrapper: as kindly suggested by Andreas Tille Closes: #701686 - d/rules: use help2man-wrapper instead of help2man to generate man pages * Imported Upstream version 2.1.0 * refreshed patches -- Alexandre Mestiashvili Wed, 27 Feb 2013 15:58:40 +0100 bowtie2 (2.0.6-1) unstable; urgency=low * Imported Upstream version 2.0.6 -- Alexandre Mestiashvili Tue, 19 Feb 2013 17:30:42 +0100 bowtie2 (2.0.5-1) unstable; urgency=low * Imported Upstream version 2.0.5 -- Alexandre Mestiashvili Fri, 11 Jan 2013 11:19:34 +0100 bowtie2 (2.0.4-1) unstable; urgency=low * Imported Upstream version 2.0.4 -- Alexandre Mestiashvili Thu, 27 Dec 2012 17:33:36 +0100 bowtie2 (2.0.2-1) unstable; urgency=low [ Carlos Borroto ] * Imported Upstream version 2.0.2 * bowtie2_gcc4.7.patch no longer needed [ Alexandre Mestiashvili ] * added autopkgtest testsuite * updated Uploaders field -- Alexandre Mestiashvili Mon, 19 Nov 2012 16:31:02 +0100 bowtie2 (2.0.0-beta7-1) unstable; urgency=low [ Alexandre Mestiashvili ] * debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and hurd-i386 SSE is not availbale on others. Closes: #668123 * debhelper version 9 * debian/rules forced hardening flags * hardening.patch to inject hardening CPPFLAGS * Imported Upstream version 2.0.0-beta7 * debian/bowtie2.lintian-overrides to avoid lintian's waring to be fixed by using epochs and tilda in upstream version -- Alexandre Mestiashvili Mon, 30 Jul 2012 13:51:31 +0200 bowtie2 (2.0.0-beta6-3) unstable; urgency=low * normalized architecture detection. For example kfreebsd-amd64 is detected as an amd64 architecture and msse flag is set.(Previous commit was wrong) (Closes: #673159) -- Alexandre Mestiashvili Fri, 01 Jun 2012 21:58:49 +0200 bowtie2 (2.0.0-beta6-2) unstable; urgency=low * debian/rules normalized output of dpkg-architecture, so for example kfreebsd-amd64 is detected as an amd64 architecture and sse flags are enabled for it. -- Alexandre Mestiashvili Thu, 31 May 2012 19:22:56 +0200 bowtie2 (2.0.0-beta6-1) unstable; urgency=low * updated debian/watch and get-orig-source to track -source suffix * Imported Upstream version 2.0.0-beta6 * debian/patches/fix_makefile_machine_detection.patch use -msse2 only for Intel architectures, Closes: #672526 -- Alexandre Mestiashvili Fri, 11 May 2012 08:41:59 +0200 bowtie2 (2.0.0-beta5-2) unstable; urgency=low [ Alexandre Mestiashvili ] * file sse_util.h has missing copyright header. The Author (Benjamin Langmead) has confirmed that the file is distributed under GPL3 license. [ Andreas Tille ] * debian/upstream: Added publication * debian/patches/fix_makefile_machine_detection.patch + debian/rules: prevent -mXX and -msse2 switches for non Intel architectures [ Alexandre Mestiashvili ] * debian/patches/bowtie2_gcc4.7.patch Closes: #672090 * updated DEP3 headers * bumperd Standards-Version to 3.9.3 * uname -m doesn't detect 32 bit chroot env - updated patcH -- Andreas Tille Thu, 26 Apr 2012 13:59:54 +0200 bowtie2 (2.0.0-beta5-1) unstable; urgency=low [ Alexandre Mestiashvili ] * Initial release (Closes: #660762) -- Alexandre Mestiashvili Wed, 22 Feb 2012 11:03:03 +0100 debian/get-orig-source0000755000000000000000000000063412162316033012127 0ustar #!/bin/sh # script to download and repack source package of bowtie which comes in zip format mkdir -p ../tarballs PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` VERSION=`uscan --verbose --force-download --repack --destdir ../tarballs| \ grep "Newest version on remote site is .* local version is .*" | \ head -n 1 | \ sed "s/Newest version on remote site is \([0-9\.]\+\)-source,.*/\1/"` debian/doc-base0000644000000000000000000000135112162316033010563 0ustar Document: bowtie2 Title: Manual for bowtie2 Author: Ben Langmead Abstract: ultrafast memory-efficient short read aligner is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Section: Science/Biology Format: html Files: /usr/share/doc/bowtie2/manual.html Index: /usr/share/doc/bowtie2/manual.html debian/upstream0000644000000000000000000000061612162316033010751 0ustar Contact: Ben Langmead Homepage: http://bowtie-bio.sourceforge.net/bowtie2/ Name: Bowtie2 Reference: Author: Ben Langmead and Steven L Salzberg Title: Fast gapped-read alignment with Bowtie 2 Journal: Nature Methods Year: 2012 Volume: 9 Pages: 357–359 DOI: 10.1038/nmeth.1923 PMID: 22388286 URL: http://www.nature.com/nmeth/journal/v9/n4/abs/nmeth.1923.html debian/rules0000755000000000000000000000205312162316033010243 0ustar #!/usr/bin/make -f pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') arch := $(shell dpkg-architecture -qDEB_HOST_ARCH 2>/dev/null | awk -F- '{print $$NF}') CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS) LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) EXTRA_FLAGS := $(LDFLAGS) # ENABLE_SSE=0 ifeq ($(arch),i386) ENABLE_SSE=1 endif ifeq ($(arch),amd64) ENABLE_SSE=1 endif %: dh $@ override_dh_auto_build: dh_auto_build -- ENABLE_SSE=$(ENABLE_SSE) EXTRA_FLAGS=$(EXTRA_FLAGS) CPPFLAGS=$(CPPFLAGS) override_dh_installman: mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/ debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align" debian/help2man-wrapper $(pkg)-build "building a colorspace index for $(pkg)" debian/help2man-wrapper $(pkg)-inspect "extracts information from a $(pkg) index" debian/help2man-wrapper $(pkg)-align "ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences" override_dh_installchangelogs: dh_installchangelogs NEWS get-orig-source: . debian/get-orig-source debian/tests/0000755000000000000000000000000012162316033010325 5ustar debian/tests/indexing-ref-genome0000755000000000000000000000066612162316033014112 0ustar #!/bin/sh set -e pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'` examplesdir=/usr/share/doc/$pkg/examples WORKDIR=$(mktemp -d) cd $WORKDIR for file in reference/lambda_virus.fa.gz reads/reads_1.fq.gz do extracted=`echo $file | awk -F/ '{print $NF}'` zcat $examplesdir/$file >${extracted%.gz} done bowtie2-build lambda_virus.fa lambda_virus >/dev/null 2>&1 bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam >/dev/null 2>&1 debian/tests/control0000644000000000000000000000003312162316033011724 0ustar Tests: indexing-ref-genome debian/compat0000644000000000000000000000000212162316033010361 0ustar 9 debian/help2man-wrapper0000755000000000000000000000132212162316033012273 0ustar #!/bin/sh # Very dirty trick to drain information via help2man even if binary outputs to stderr if [ $# -ne 2 ] ; then echo "Usage: $0 " exit 1 fi pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'` version=`dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d-` mandir=${PWD}/debian/${pkg}/usr/share/man/man1/ tmpdir=`mktemp -d` mkdir -p $tmpdir binname=$1 tmpbin=${tmpdir}/$binname echo "#!/bin/sh" > $tmpbin echo "cat <> $tmpbin ${PWD}/debian/${pkg}/usr/bin/$binname 2>> $tmpbin chmod 755 $tmpbin help2man --no-info --help-option="''" --no-discard-stderr --name="$2" --version-string="${version}" $tmpbin > $mandir/${binname}.1 rm -rf $tmpdir debian/control0000644000000000000000000000366212162316033010575 0ustar Source: bowtie2 Section: science Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Alexandre Mestiashvili , Andreas Tille , Carlos Borroto Build-Depends: debhelper (>= 9.0), help2man Standards-Version: 3.9.4 XS-Testsuite: autopkgtest Homepage: http://bowtie-bio.sourceforge.net/bowtie2 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/bowtie2.git Vcs-Git: git://anonscm.debian.org/debian-med/bowtie2.git Package: bowtie2 Architecture: amd64 i386 hurd-i386 kfreebsd-amd64 kfreebsd-i386 Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: bowtie2-examples Description: ultrafast memory-efficient short read aligner is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. . Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes Package: bowtie2-examples Architecture: all Depends: ${misc:Depends} Recommends: bowtie2 Enhances: bowtie2 Description: Examples for bowtie2 An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. . Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes . This package provides some example data to work with bowtie2. debian/bowtie2-examples.install0000644000000000000000000000027212162316033013743 0ustar example/reads usr/share/doc/bowtie2/examples example/index usr/share/doc/bowtie2/examples example/reference usr/share/doc/bowtie2/examples scripts usr/share/doc/bowtie2/examples debian/source/0000755000000000000000000000000012162316033010463 5ustar debian/source/format0000644000000000000000000000001412162316033011671 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000012162316033010612 5ustar debian/patches/series0000644000000000000000000000006512162316033012030 0ustar hardening.patch fix_makefile_machine_detection.patch debian/patches/fix_makefile_machine_detection.patch0000644000000000000000000000246312162316033020005 0ustar Subject: Attemp to adapt the build flags to built package on all supported architectures. Origin: Debian Med Packaging Team Date: 2013-02-28 --- bowtie2.orig/Makefile +++ bowtie2/Makefile @@ -117,27 +117,29 @@ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c) VERSION = $(shell cat VERSION) -# Convert BITS=?? to a -m flag -BITS=32 -ifeq (x86_64,$(shell uname -m)) -BITS=64 -endif -# msys will always be 32 bit so look at the cpu arch instead. -ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432))) - ifeq (1,$(MINGW)) - BITS=64 - endif -endif -BITS_FLAG = - -ifeq (32,$(BITS)) - BITS_FLAG = -m32 -endif +ifeq (1,$(ENABLE_SSE)) + ARCH := $(shell getconf LONG_BIT) + UNAME := $(shell uname -m ) + # Convert BITS=?? to a -m flag + BITS=32 + BITS_FLAG = -m32 + ifeq (64,$(ARCH)) + BITS=64 + BITS_FLAG = -m64 + endif + ifeq ($(UNAME),'Power Macintosh') + ifeq (32,$(BITS)) + BITS_FLAG = -m32 + SSE_FLAG = + endif + ifeq (64,$(BITS)) + BITS_FLAG = -m64 + SSE_FLAG = + endif + endif -ifeq (64,$(BITS)) - BITS_FLAG = -m64 + SSE_FLAG=-msse2 endif -SSE_FLAG=-msse2 DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG) DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" debian/patches/hardening.patch0000644000000000000000000000052112162316033013570 0ustar Subject: Patch injects hardening CPPFLAGS Origin: Debian Med Packaging Team --- bowtie2.orig/Makefile +++ bowtie2/Makefile @@ -204,7 +204,8 @@ $(FILE_FLAGS) \ $(PREF_DEF) \ $(MM_DEF) \ - $(SHMEM_DEF) + $(SHMEM_DEF)\ + $(CPPFLAGS) # # bowtie2-build targets debian/bowtie2.dirs0000644000000000000000000000002312162316033011414 0ustar usr/share/man/man1 debian/copyright0000644000000000000000000000532012162316033011116 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Bowtie2 Upstream-Contact: Ben Langmead Source: http://sourceforge.net/projects/bowtie2-bio/files/bowtie2/ Files: * Copyright: © 2009-2011 Ben Langmead, C. Trapnell, M. Pop, Steven L. Salzberg License: GPL-3.0+ Files: fast_mutex.h Copyright: © 2010-2012, Marcus Geelnard License: Zlib Files: tinythread.* Copyright: © 2010-2012, Marcus Geelnard License: Zlib Files: ls.h Copyright: © 1999, N. Jesper Larsson License: This file contains an implementation of the algorithm presented in "Faster Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko Sadakane (sada@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: debian/* Copyright: © 2012 Alexandre Mestiashvili License: GPL-3.0+ License: GPL-3.0+ 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 3 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 3 can be found in "/usr/share/common-licenses/GPL-3". 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. debian/bowtie2.docs0000644000000000000000000000010412162316033011403 0ustar MANUAL TUTORIAL doc/manual.html doc/style.css doc/strip_markdown.pl debian/gbp.conf0000644000000000000000000000017412162316033010604 0ustar # This source package is managed with git-buildpackage and pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True