Imported Debian patch 0.12.7-3

diff --git a/debian/README.source b/debian/README.source
new file mode 100644 (file)
index 0000000..68f4938
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,12 @@
+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.
+

diff --git a/debian/bowtie-examples.install b/debian/bowtie-examples.install
new file mode 100644 (file)
index 0000000..24069c3
--- /dev/null
+++ b/debian/bowtie-examples.install
@@ -0,0 +1,2 @@
+genomes  usr/share/doc/bowtie/examples
+indexes  usr/share/doc/bowtie/examples

diff --git a/debian/bowtie.dirs b/debian/bowtie.dirs
new file mode 100644 (file)
index 0000000..fcf16f2
--- /dev/null
+++ b/debian/bowtie.dirs
@@ -0,0 +1 @@
+usr/share/man/man1

diff --git a/debian/bowtie.docs b/debian/bowtie.docs
new file mode 100644 (file)
index 0000000..b012f25
--- /dev/null
+++ b/debian/bowtie.docs
@@ -0,0 +1,5 @@
+NEWS
+MANUAL
+TUTORIAL
+doc/manual.html
+doc/style.css

diff --git a/debian/bowtie.install b/debian/bowtie.install
new file mode 100644 (file)
index 0000000..47883be
--- /dev/null
+++ b/debian/bowtie.install
@@ -0,0 +1,4 @@
+bowtie         usr/bin
+bowtie-build   usr/bin
+bowtie-inspect  usr/bin
+bowtie*-debug   usr/bin

diff --git a/debian/bowtie.links b/debian/bowtie.links
new file mode 100644 (file)
index 0000000..13e198c
--- /dev/null
+++ b/debian/bowtie.links
@@ -0,0 +1,3 @@
+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

diff --git a/debian/changelog b/debian/changelog
new file mode 100644 (file)
index 0000000..8c0543a
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,34 @@
+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

diff --git a/debian/compat b/debian/compat
new file mode 100644 (file)
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9

diff --git a/debian/control b/debian/control
new file mode 100644 (file)
index 0000000..1b71f1c
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,48 @@
+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.

diff --git a/debian/copyright b/debian/copyright
new file mode 100644 (file)
index 0000000..a3eef72
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,61 @@
+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
+

diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644 (file)
index 0000000..da8dcb9
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,19 @@
+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

diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100644 (file)
index 0000000..a61aacb
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,22 @@
+#!/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}"
+

diff --git a/debian/patches/gcc-4.7.patch b/debian/patches/gcc-4.7.patch
new file mode 100644 (file)
index 0000000..adcb91d
--- /dev/null
+++ b/debian/patches/gcc-4.7.patch
@@ -0,0 +1,49 @@
+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.
+  */

diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644 (file)
index 0000000..9982159
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+gcc-4.7.patch
+use-dpkg-buildflags.patch

diff --git a/debian/patches/use-dpkg-buildflags.patch b/debian/patches/use-dpkg-buildflags.patch
new file mode 100644 (file)
index 0000000..146fe49
--- /dev/null
+++ b/debian/patches/use-dpkg-buildflags.patch
@@ -0,0 +1,17 @@
+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)\""
+ 

diff --git a/debian/patches/use_debian_seqan.patch b/debian/patches/use_debian_seqan.patch
new file mode 100644 (file)
index 0000000..53c9519
--- /dev/null
+++ b/debian/patches/use_debian_seqan.patch
@@ -0,0 +1,26 @@
+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)

diff --git a/debian/rules b/debian/rules
new file mode 100755 (executable)
index 0000000..99e705b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,32 @@
+#!/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

diff --git a/debian/source/format b/debian/source/format
new file mode 100644 (file)
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)

diff --git a/debian/upstream b/debian/upstream
new file mode 100644 (file)
index 0000000..da7568a
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,10 @@
+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

diff --git a/debian/watch b/debian/watch
new file mode 100644 (file)
index 0000000..e63fb24
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/bowtie-bio/bowtie-([\d\.]+)-src\.zip