--- /dev/null
+bowtie for Debian
+-----------------
+
+The bowtie package seems to rely on version 1.1 of the seqan library,
+while Debian otherwise already features version 1.2. It yet remains
+to be investigated, to what degree the two might possibly be
+compatible.
+
+We did not dare any respective experiments and hope for a clarification
+by upstream on this issue - we just should not introduce any hidden
+mistakes here.
+
--- /dev/null
+genomes usr/share/doc/bowtie/examples
+indexes usr/share/doc/bowtie/examples
--- /dev/null
+usr/share/man/man1
--- /dev/null
+NEWS
+MANUAL
+TUTORIAL
+doc/manual.html
+doc/style.css
--- /dev/null
+bowtie usr/bin
+bowtie-build usr/bin
+bowtie-inspect usr/bin
+bowtie*-debug usr/bin
--- /dev/null
+usr/share/man/man1/bowtie.1.gz usr/share/man/man1/bowtie-debug.1.gz
+usr/share/man/man1/bowtie-build.1.gz usr/share/man/man1/bowtie-build-debug.1.gz
+usr/share/man/man1/bowtie-inspect.1.gz usr/share/man/man1/bowtie-inspect-debug.1.gz
--- /dev/null
+bowtie (0.12.7-3) unstable; urgency=low
+
+ * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
+ hardening flags (thanks for the patch to Simon Ruderich
+ <simon@ruderich.org>)
+ Closes: #670230
+
+ -- Andreas Tille <tille@debian.org> Tue, 24 Apr 2012 13:21:32 +0200
+
+bowtie (0.12.7-2) unstable; urgency=low
+
+ * Do not give a pointer to non existing info pages in manpages
+ * debian/control:
+ - fixed Vcs fields
+ - Standards-Version: 3.9.3 (no changes needed)
+ * debian/upstream: Add citation information
+ * debian/rules: calculate pkg name instead of setting it
+ * debian/copyright: DEP5 verified using
+ cme fix dpkg-copyright
+ * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
+ the function is used
+ Thanks to Rodolfo García Peñas <kix@kix.es> and
+ gregor herrmann <gregoa@debian.org>
+ Closes: #667120
+ * debhelper 9 (control+compat)
+ Hardening flags were explicitly tested but not enforced in debian/rules
+
+ -- Andreas Tille <tille@debian.org> Sun, 22 Apr 2012 21:09:05 +0200
+
+bowtie (0.12.7-1) unstable; urgency=low
+
+ * Initial release (Closes: #604940)
+
+ -- Andreas Tille <tille@debian.org> Wed, 02 Feb 2011 13:47:12 +0100
--- /dev/null
+Source: bowtie
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller@debian.org>,
+ Yask Gupta <yask.gupta87@gmail.com>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 9), help2man
+Standards-Version: 3.9.3
+Homepage: http://bowtie-bio.sourceforge.net/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bowtie/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bowtie/trunk/
+
+Package: bowtie
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: bowtie-examples
+Description: ultrafast memory-efficient short read aligner
+ This package addresses the problem to interpret the results from the
+ latest (2010) DNA sequencing technologies. Those will yield fairly
+ short stretches and those cannot be interpreted directly. It is the
+ challenge for tools like Bowtie to give a chromosomal location to the
+ short stretches of DNA sequenced per run.
+ .
+ Bowtie aligns short DNA sequences (reads) to the human genome at a rate
+ of over 25 million 35-bp reads per hour. Bowtie indexes the genome with
+ a Burrows-Wheeler index to keep its memory footprint small: typically
+ about 2.2 GB for the human genome (2.9 GB for paired-end).
+
+Package: bowtie-examples
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: bowtie
+Enhances: bowtie
+Description: Examples for bowtie, the ultrafast memory-efficient short read aligner
+ This package addresses the problem to interpret the results from the
+ latest (2010) DNA sequencing technologies. Those will yield fairly
+ short stretches and those cannot be interpreted directly. It is the
+ challenge for tools like Bowtie to give a chromosomal location to the
+ short stretches of DNA sequenced per run.
+ .
+ Bowtie aligns short DNA sequences (reads) to the human genome at a rate
+ of over 25 million 35-bp reads per hour. Bowtie indexes the genome with
+ a Burrows-Wheeler index to keep its memory footprint small: typically
+ about 2.2 GB for the human genome (2.9 GB for paired-end).
+ .
+ This package provides some example data to work with bowtie.
--- /dev/null
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Bowtie
+Upstream-Contact: Ben Langmead <blangmea@jhsph.edu>
+Source: http://sourceforge.net/projects/bowtie-bio/files/bowtie/
+
+Files: *
+Copyright: © 2009-2010 Ben Langmead, C. Trapnell, M. Pop, Steven L. Salzberg
+License: Artistic
+
+Files: SeqAn-1.1
+Copyright: 2007-2009 Andreas Döring <doering@inf.fu-berlin.de>,
+ David Weese <weese@inf.fu-berlin.de>,
+ Tobias Rausch <rausch@inf.fu-berlin.de>,
+ Stephan Aiche <aiche@inf.fu-berlin.de>,
+ Anne-Katrin Emde <emde@inf.fu-berlin.de>,
+ Carsten Kemena <kemena@inf.fu-berlin.de>,
+ Konrad Ludwig Moritz Rudolph <krudolph@inf.fu-berlin.de>,
+ Marcel H. Schulz. <marcel.schulz@molgen.mpg.de>
+License: LGPL-3+
+
+Files: debian/*
+Copyright: © 2011 Steffen Moeller <moeller@debian.org>,
+ Yask Gupta <yask.gupta87@gmail.com>
+ © 2011 Andreas Tille <tille@debian.org>
+License: LGPL-3+
+
+Files: SeqAn-1.1/seqan/index/index_sa_lss.h
+Copyright: 1999 N. Jesper Larsson <jesper@cs.lth.se>
+ 2007 David Weese.
+License: other
+ 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.
+
+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 Debian.
+ .
+ THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
+ OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ .
+ On Debian systems, the complete text of the Artistic License
+ can be found in "/usr/share/common-licenses/Artistic".
+
+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, you can find the LGPL license in:
+ /usr/share/common-licenses/LGPL
+
--- /dev/null
+Document: bowtie
+Title: Manual for bowtie
+Author: Ben Langmead
+Abstract: ultrafast memory-efficient short read aligner
+ Bowtie is an ultrafast, memory-efficient short read aligner geared toward
+ quickly aligning large sets of short DNA sequences (reads) to large genomes. It
+ aligns 35-base-pair reads to the human genome at a rate of 25 million reads per
+ hour on a typical workstation. Bowtie indexes the genome with a Burrows-Wheeler
+ index to keep its memory footprint small: for the human genome, the index is
+ typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or
+ colorspace alignment). Multiple processors can be used simultaneously to
+ achieve greater alignment speed. Bowtie can also output alignments in the
+ standard SAM format, allowing Bowtie to interoperate with other tools
+ supporting SAM, including the SAMtools consensus, SNP, and indel callers.
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/bowtie/manual.html
+Index: /usr/share/doc/bowtie/manual.html
--- /dev/null
+#!/bin/sh
+# script to download and repack source package of bowtie which comes in zip format
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download | \
+ grep "Newest version on remote site is .* local version is .*" | \
+ head -n 1 | \
+ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+UPSTREAMDIR=${PKG}-${VERSION}
+unzip ../"${UPSTREAMDIR}-src.zip"
+
+## remove copy of SeqAn library - unfortunately the package does not compile
+## with the Debian packaged version 1.2
+#rm -rf "${UPSTREAMDIR}"/SeqAn-1.1
+
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}"
+rm -rf "${UPSTREAMDIR}"
+
--- /dev/null
+Author: gregor herrmann <gregoa@debian.org>,
+Date: Sun, 22 Apr 2012 22:27:51 +0200
+Bug-Closed: http://bugs.debian.org/667120
+Description: function "reverseInPlace" is declared after the function is used
+ For more detailed information see
+ http://lists.debian.org/debian-mentors/2012/04/msg00409.html
+ and other mails in this thread.
+
+--- bowtie-0.12.7.orig/alphabet.h
++++ bowtie-0.12.7/alphabet.h
+@@ -41,6 +41,19 @@
+ /**
+ * Reverse-complement s in-place. Ns go to Ns.
+ */
++
++/// Reverse a string in-place
++template <typename TStr>
++static inline void reverseInPlace(TStr& s) {
++ typedef typename Value<TStr>::Type TVal;
++ size_t len = length(s);
++ for(size_t i = 0; i < (len>>1); i++) {
++ TVal tmp = s[i];
++ s[i] = s[len-i-1];
++ s[len-i-1] = tmp;
++ }
++}
++
+ template<typename TStr>
+ static inline void reverseComplementInPlace(TStr& s, bool color) {
+ typedef typename Value<TStr>::Type TVal;
+@@ -69,18 +82,6 @@
+ }
+ }
+
+-/// Reverse a string in-place
+-template <typename TStr>
+-static inline void reverseInPlace(TStr& s) {
+- typedef typename Value<TStr>::Type TVal;
+- size_t len = length(s);
+- for(size_t i = 0; i < (len>>1); i++) {
+- TVal tmp = s[i];
+- s[i] = s[len-i-1];
+- s[len-i-1] = tmp;
+- }
+-}
+-
+ /**
+ * Return the reverse-complement of s.
+ */
--- /dev/null
+gcc-4.7.patch
+use-dpkg-buildflags.patch
--- /dev/null
+Description: Use build flags from environment (dpkg-buildflags).
+ Necessary for hardening flags.
+Author: Simon Ruderich <simon@ruderich.org>
+Last-Update: 2012-04-24
+Bug-Closed: http://bugs.debian.org/670230
+
+--- bowtie-0.12.7.orig/Makefile
++++ bowtie-0.12.7/Makefile
+@@ -177,7 +177,7 @@
+ cat $^ | md5sum | awk '{print $$1}' > .$@.md5
+ endef
+
+-ALL_FLAGS=$(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
++ALL_FLAGS=$(EXTRA_FLAGS) $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS)
+ DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
+ RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
+
--- /dev/null
+Note: This patch is deactivated because the Debian packaged version of SeqAn 1.2
+ is not compatible with the version included into this package
+
+Author: Andreas Tille <tilleqdebian.org>
+Date: 2011-01-30
+Description: Use Debian packages SeqAn Librariy instead of copy in upstream source
+--- bowtie-0.12.7.orig/Makefile
++++ bowtie-0.12.7/Makefile
+@@ -2,7 +2,7 @@
+ # Makefile for bowtie, bowtie-build, bowtie-inspect
+ #
+
+-SEQAN_DIR = SeqAn-1.1
++SEQAN_DIR = /usr/include/seqan
+ SEQAN_INC = -I $(SEQAN_DIR)
+ INC = $(SEQAN_INC)
+ GCC_PREFIX = $(shell dirname `which gcc`)
+@@ -149,8 +149,6 @@
+ $(wildcard *.hh) \
+ $(wildcard *.c) \
+ $(wildcard *.cpp) \
+- $(shell $(FIND) SeqAn-1.1 -name "*.h") \
+- $(shell $(FIND) SeqAn-1.1 -name "*.txt") \
+ doc/strip_markdown.pl \
+ Makefile \
+ $(GENERAL_LIST)
--- /dev/null
+#!/usr/bin/make -f
+# debian/rules for bowtie
+# Andreas Tille <tille@debian.org>
+# GPL
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ $(MAKE) allall
+
+override_dh_auto_install:
+ help2man --name="ultrafast memory-efficient short read aligner" --no-info \
+ $(CURDIR)/bowtie > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie.1
+ help2man --name="building a colorspace index for bowtie" --no-info \
+ $(CURDIR)/bowtie-build > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie-build.1
+ help2man --name="extracts information from a bowtie index" --no-info \
+ $(CURDIR)/bowtie-inspect > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie-inspect.1
+
+override_dh_auto_clean:
+ rm -f .bowtie*
+ dh_auto_clean
+
+get-orig-source:
+ . debian/get-orig-source
--- /dev/null
+3.0 (quilt)
--- /dev/null
+Reference:
+ author: Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg
+ title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
+ journal: Genome Biology
+ volume: 10
+ pages: R25
+ year: 2009
+ DOI: 10.1186/gb-2009-10-3-r25
+ URL: http://genomebiology.com/2009/10/3/R25
+ eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf
--- /dev/null
+version=3
+http://sf.net/bowtie-bio/bowtie-([\d\.]+)-src\.zip