debian/0000755000000000000000000000000012176666446007210 5ustar debian/velvet.doc-base0000644000000000000000000000036311545031301012065 0ustar Document: velvet Title: Velvet Manual Author: Daniel Zerbino Abstract: This manual describes how to install, use and tweak Velvet, a short sequence read assembler. Section: Science/Biology Format: PDF Files: /usr/share/doc/velvet/Manual.pdf debian/control0000644000000000000000000000365212176660131010602 0ustar Source: velvet Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), zlib1g-dev, help2man, texlive-latex-base Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/velvet/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/velvet/trunk/ Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Package: velvet Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: velvet-example Description: Nucleic acid sequence assembler for very short reads Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. Package: velvet-example Architecture: all Depends: ${misc:Depends} Recommends: python Description: Example data for the Velvet sequence assembler Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. . Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs. . This package contains the example data distributed in the sources of Velvet, a de novo genomic assembler. debian/install0000644000000000000000000000010211711104602010541 0ustar velvet* usr/bin shuffl* usr/share/velvet contrib usr/share/velvet debian/README.source0000644000000000000000000000204312176653155011357 0ustar Repacked source package. ──────────────────────── The original sources were downloaded from http://www.ebi.ac.uk/~zerbino/velvet/ and repacked after removing the third-party directory in order to not have to document all copyright notices in third-party/zlib-1.2.3. The resulting upstream source tarball version was appended by '+dfsg' because it is a frequently used appendix when repackaging. It does not mean that velvet was not dfsg free in the original form - it just says the Debian upstream tarball is definitely dfsg free and is different from what can be downloaded at velvet homepage. Since version 1.0.2 of velvet the source tarball contains an extra copy of a velvet extension called MetaVelvet. There is a lot of duplicated code which was removed from the tarball to simplify the build system of the Debian package. The latest version of MetaVelvet can always be downloaded here: https://github.com/hacchy/MetaVelvet -- Andreas Tille Thu, 01 Aug 2013 14:33:28 +0200 debian/rules0000755000000000000000000000324712176666162010271 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ pkg=velvet override_dh_auto_clean : dh_auto_clean rm -rf zlib override_dh_auto_build : touch zlib # prevents the zlib in the ‘third-party’ folder to be built. dh_auto_build -- OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" dh_auto_build -- color OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" override_dh_install : mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/ help2man --no-info --name="simple hashing program" \ $(CURDIR)/velveth > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth.1 help2man --no-info --name="simple hashing program (colorspace version)" \ $(CURDIR)/velveth_de > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth_de.1 help2man --no-info --version-option=" " \ --name="de Bruijn graph construction, error removal and repeat resolution" \ $(CURDIR)/velvetg > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg.1 help2man --no-info --version-option=" " \ --name="de Bruijn graph construction, error removal and repeat resolution (colorspace version)" \ $(CURDIR)/velvetg_de > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velvetg_de.1 dh_install rm -rf $(CURDIR)/debian/$(pkg)/usr/share/velvet/contrib/MetaVelvet-v0.3.1/obj # remove extra copies of GPL find $(CURDIR)/debian -type f -name 'LICENSE*' -delete #Prevent compression of user manual override_dh_compress : dh_compress -X.pdf override_dh_pysupport : #Not needed, Python scripts are just for examples override_dh_builddeb: dh_builddeb -- -Z xz get-orig-source: . debian/get-orig-source debian/watch0000644000000000000000000000016612022361117010215 0ustar version=3 opts=dversionmangle=s/([~+]dfsg|~nozlibcopy)// \ http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz debian/upstream0000644000000000000000000000116311724071647010763 0ustar Contact: Daniel Zerbino Reference-DOI: 10.1101/gr.074492.107 Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Name: Velvet Reference-PMID: 18349386 Reference: author: Zerbino, Daniel R. and Birney, Ewan title: > Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal: Genome Research volume: 18 number: 5 pages: 821-829 year: 2008 URL: http://genome.cshlp.org/content/18/5/821.abstract eprint: http://genome.cshlp.org/content/18/5/821.full.pdf+html Repository: http://github.com/dzerbino/velvet Watch: http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz debian/copyright0000644000000000000000000001063312176662423011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Velvet Upstream-Contact: Daniel Zerbino Source: http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz Upstream sources are modified by removing the “third-party” directory, which contains a convenience copy of the Zlib. Files-Excluded: third-party *.o .DS_Store debian contrib/MetaVelvet-1.2.01/ISGraph/*.a ._* */._* */*/._* */*/.hg_* Files: * Copyright: © 2006-2011 Daniel Zerbino © 2000-2005 Guy St.C. Slater © 2009 John Marshall © 2009 David Studholme © 2011 Convey Computer Corporation (info@conveycomputer.com) License: GPL-2+ Files: src/fibpriv.h src/dfib.c src/fib.h src/fib.c src/dfib.h src/dfibpriv.h Copyright: © 1997, 1999-2003 John-Mark Gurney. License: FreeBSD-like Redistribution and use in source and binary forms, with or without . are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: contrib/afg_handling/* contrib/VelvetOptimiser/* Copyright: © 2008,2009 Simon Gladman License: GPL-2+ Files: contrib/layout/* Copyright: © 2008 Paul Harrison (pfh@logarithmic.net) License: GPL-2+ Files: contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl contrib/observed-insert-length.pl/observed-insert-length.pl contrib/show_repeats/show_repeats.pl Copyright: 2009, Torsten Seemann 2009, Daniel Zerbino License: GPL-3+ This program 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 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, see . Comment: On Debian systems, the complete text of the GNU General Public License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’. Files: debian/* Copyright: 2008-2009 Charles Plessy 2008-2011 Andreas Tille 2011 Tim Booth License: Same The packaging work is licensed under the same terms as Velvet itself. License: GPL-2+ Velvet 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. . Velvet 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 Velvet; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Comment: 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/source/0000755000000000000000000000000012176652361010477 5ustar debian/source/format0000644000000000000000000000001411545031301011665 0ustar 3.0 (quilt) debian/get-orig-source0000644000000000000000000000265412176451622012141 0ustar #!/bin/sh # script to download and repack source package of velvet # this is needed to remove a copy of zlib if uscan --help | grep -q -- --repack-compression ; then echo "Use new enhanced uscan" uscan --verbose --force-download --repack-compression xz exit fi 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}" mv ../${UPSTREAMDIR}.tgz . tar -xzf ${UPSTREAMDIR}.tgz rm -rf ${UPSTREAMDIR}/third-party ## Delete useless binaries once we are changing the original tarball anyway # delete precompiled object files # rm -f ${UPSTREAMDIR}/obj/*.o find ${UPSTREAMDIR} -name "*.o" -exec rm -f \{\} \; # delete .DS_Store files find ${UPSTREAMDIR} -name .DS_Store -exec rm -f \{\} \; rm -rf ${UPSTREAMDIR}/contrib/MetaVelvet-1.2.01/ISGraph/*.a ## remove separate project which is basically a duplication of velvet code ## this should be packaged separately with an up to date version #rm -rf ${UPSTREAMDIR}/contrib/MetaVelvet* # ... don't do this any more SUFFIX="+dfsg" mv ${UPSTREAMDIR} ${UPSTREAMDIR}${SUFFIX} rm -f ../"$PKG"_"$VERSION".orig.tar.gz tar -cJf ../"$PKG"_"$VERSION~nozlibcopy".orig.tar.xz "${UPSTREAMDIR}${SUFFIX}" rm -rf "${UPSTREAMDIR}${SUFFIX}" debian/README.Debian0000644000000000000000000000033412176660221011232 0ustar Velvet for Debian ----------------- Third party scripts have been placed in ‘/usr/share/doc/velvet/contrib’ inside the velvet-example package. -- Andreas Tille Thu, 01 Aug 2013 14:33:28 +0200 debian/changelog0000644000000000000000000002713212176666273011065 0ustar velvet (1.2.10+dfsg-1) unstable; urgency=low * New upstream version (+adapted patch) * debian/watch: cope with +dfsg suffix (in addition to old ~nozlibcopy) * debian/get-orig-source: - Enable simple changing of suffix for repackaged source - Check for existence of enhanced uscan and use it if available for easier repackaging * debian/control: - cme fix dpkg-control - no explicit quilt Build-Depends (also removed from rules) - bumped python from Recommends to Depends because there are Python scripts installed in velvet/contrib - use anonscm in Vcs fields * debian/copyright: Add Files-Excluded to document what was removed from original source * rename debian/{docs,install} to debian/velvet.{docs,install} which is more safe in the case of multibinary package * debian/velvet.install: shuffle* files are in contrib directory now * debhelper 9 (control+compat) to enable hardening options * debian/rules: propagate hardening options * debian/copyright: - Files-Excluded: Exclude MAXOS internal files cruft from upstream archive - Adapt Source location * debian/README.source: Updated explanation for repackaging, droped some outdated information * debian/rules: - Do not try to rmdir nonexisting directory - Remove extra copies of GPL * debian/velvet-examples.install: use install instead of examples to move the examples into /usr/share/doc/velvet directly. Also all contrib stuff was moved here to not bloat main velvet binary package with potentially unused stuff in /usr/share * debian/README.Debian: document move of contrib stuff -- Andreas Tille Thu, 01 Aug 2013 14:33:28 +0200 velvet (1.2.03~nozlibcopy-1) unstable; urgency=low * New upstream release. * Updated debian/patches/include_debians_zlib.patch. -- Charles Plessy Thu, 16 Feb 2012 13:37:19 +0900 velvet (1.1.07~nozlibcopy-1) unstable; urgency=low * New upstream release (Closes: #647415). * debian/contol: - Pre-Depends on dpkg (>= 1.15.6) for Ubuntu LTS. - Removed Multi-Arch: foreign. -- Charles Plessy Fri, 09 Dec 2011 14:07:58 +0900 velvet (1.1.06~nozlibcopy-1) unstable; urgency=low [ Andreas Tille ] * New upstream version * debian/copyright: Revised * debian/get-orig-source: Do not remove MetaVelvet * debian/control: Build-Depends: texlive-latex-base [ Charles Plessy ] * Corrected VCS URLs in debian/control. * Compress source and binary packages with xz (debian/rules, debian/get-orig-source). * Turn on multithreading with OpenMP (debian/rules). * Remove empty directory contrib/MetaVelvet-v0.3.1/obj (debian/rules). -- Charles Plessy Tue, 27 Sep 2011 15:12:41 +0900 velvet (1.1.05-1ubuntu4) lucid; urgency=low * Moved from CDBS to DH * New upstream. Still includes a copy of Zlib but the default is now to use the system version, so removed relevant patch. * Modified build to work on unmodified upstream (still works on pruned upstream). -- Tim Booth Thu, 11 Aug 2011 13:34:46 +0100 velvet (1.1.02~nozlibcopy-1) unstable; urgency=low * New upstream version upgraded patches, tweak $(LIBS) into Z_LIB_FILES variable of Makefile which makes patch more robust against upstream changes * Debhelper 8 (control+compat) * debian/rules: Leave out Z_LIB_FILES in parameter list * debian/get-orig-source: Once we are rebuilding the original tarball anyway it makes sense to remove an outdated copy of MetaVelvet and replace it rather by a hint to the currently maintained source in README.source * Standards-Version: 3.9.2 (no changes needed) -- Andreas Tille Fri, 15 Apr 2011 10:51:16 +0200 velvet (1.0.18~nozlibcopy-1) unstable; urgency=low * New upstream version * debian/get-orig-source: Make sure MD5sum stays the same for different download -- Andreas Tille Wed, 19 Jan 2011 08:48:19 +0100 velvet (1.0.15~nozlibcopy-2) unstable; urgency=low * Fix FTBFS with ld --as-needed (thanks for the patch to Matthias Klose) Closes: #607535 -- Andreas Tille Mon, 20 Dec 2010 08:43:16 +0100 velvet (1.0.15~nozlibcopy-1) unstable; urgency=low * New upstream source * Standards-Version: 3.9.1 (no changes needed) * debian/get-upstream-source: Remove precompiled *.o files and .DS_Store files once we are repackaging anyway * debian/patches/fix-perl-path.patch: Fix Perl path -- Andreas Tille Wed, 24 Nov 2010 15:42:33 +0100 velvet (1.0.02~nozlibcopy-1) unstable; urgency=low * New upstream version * Source format 3.0 (quilt) * debian/control: - Recommends: python (some new scripts in /usr/share/velvet/contrib are Python scripts) - Build-Depends: quilt * debian/rules: include /usr/share/cdbs/1/rules/patchsys-quilt.mk (instead of simple-patchsys) * debian/patches: Switch to quilt * debian/patches/shuffleSequences_fasta.patch: Add interpreter to Python script -- Andreas Tille Thu, 24 Jun 2010 15:41:53 +0200 velvet (0.7.61~nozlibcopy-1) unstable; urgency=low * New upstream version * debian/get-orig-source, debian/rules: Strip zlib copy from upstream tarball -- Andreas Tille Mon, 22 Mar 2010 15:41:53 +0100 velvet (0.7.59~nozlibcopy-1) unstable; urgency=low * New upstream release [ Charles Plessy ] * Incremented Standard-Version in debian/control to reflect conformance with Policy 3.8.4 (no changes needed). [ Andreas Tille ] * Fixed watch file to make sure it is not supporting newer upstream -- Charles Plessy Sat, 20 Feb 2010 13:00:13 +0900 velvet (0.7.56~nozlibcopy-1) unstable; urgency=low * New upstream version. * Repackaged the upstream directory to remove the convenience copy of the zlib. Documented this in ‘debian/README.source’. Closes: #561433. * Updated debian/copyright. * Added ‘include_debians_zlib.patch’ to enforce the use of /usr/include/zlib.h. This patch is applied using CDBS, see ‘debian/rules’ and ‘debian/README.source’. * Renamed ‘debian/reference’ ‘debian/upstream-metadata.yaml’ and centralised upstream-specific information there. -- Charles Plessy Mon, 25 Jan 2010 13:03:06 +0900 velvet (0.7.55-1) unstable; urgency=low * New upstream version -- Andreas Tille Fri, 25 Sep 2009 14:52:41 +0200 velvet (0.7.53-1) unstable; urgency=low * New upstream release: - Ignored reads in Pebble corrected - Added automatic measure of median coverage and median insert length - Updated manual to cover the above -- Charles Plessy Fri, 04 Sep 2009 13:42:22 +0900 velvet (0.7.52-1) unstable; urgency=low * New upstream release: V 0.7.51 - Small parsing bug - Correction to the observed-insert-length script - Verified strncpy calls - NCBI friendly 10bp N-gaps V 0.7.52 - Crashing bug when parsing fa.gz files - Crashing bug with tiny Graph files - Bug when loading FASTA files with short lines - Corrected snp_view.pl script to write reverse strand reads in snp_view_reads file - Corrected snp_view.pl script to behave better near the edges of contigs - Updated observed_insert_length to compute the standard deviation of the set - Corrected observed_insert_length script so that it does not crash on empty libraries - Crashing bug when providing an odd number of paired reads - Mapping bug of reads during tour bus correction * Replaced the UNRELEASED tag by ‘unstable’ in debian/changelog as 0.7.50-1 was really uploaded and accepted by the archive. -- Charles Plessy Thu, 03 Sep 2009 20:00:54 +0900 velvet (0.7.50-1) unstable; urgency=low * New upstream release: V 0.7.49 - Added the optional output of unused reads - Added David Studholme's FastA -> AGP script V 0.7.50 - Added the extractContigReads script - Updated the FastA -> AGP script - Added the observed-insert-length script - Small parsing bug in simplified read import * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.3 (no changes needed). -- Charles Plessy Wed, 19 Aug 2009 21:58:49 +0900 velvet (0.7.48-1) unstable; urgency=low * New upstream release: - Accelerated concatenation (pre-graph and graph) - Unlimited contig size - Bug in parsing FASTA files with very long lines - Parsing bug in snp_view.pl script -- Charles Plessy Tue, 11 Aug 2009 19:54:03 +0900 velvet (0.7.47-1) unstable; urgency=low * New upstream release correcting bugs and enhancing documentation. * Multi-Arch support (‘foreign’) in debian/control. * Corrected debian/install to avoid ugly ‘contrib/contrib’ location. -- Charles Plessy Thu, 30 Jul 2009 13:43:13 +0900 velvet (0.7.44-1) unstable; urgency=low * New upstream release. * Added bibliographic information in BibTeX format in debian/references. * debian/rules: touch zlib to avoid third-party zlib to be built. * Removed ‘debian/patches/20_external_zlib.patch’. Passing apropriate variables in debian/rules is enough to build dynamically on Debian's zlib. * Removed the quilt patch system (debian/control, debian/README.source debian/rules). * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.2 (no changes needed). * Corrected the installation of files that were moved from the ‘third-party’ directory to the ‘contrib’ directory. * Experimentation on debian/copyright. -- Charles Plessy Sun, 12 Jul 2009 00:24:56 +0900 velvet (0.7.37-1) unstable; urgency=low * New upstream release. - Small formatting change to error messages - K > 31 now possible - --help option corrected for velvetg - Acceleration of k-mer operations (comparable to 64bit int performance) - Fixed variable lengths - Reordered struct declaration for more efficent memory alignment * debian/rules: - Restored manpage generation for velvetg*. - Added forgotten CFLAGS for the colorspace building. -- Charles Plessy Sat, 27 Jun 2009 12:27:27 +0900 velvet (0.7.34-1) unstable; urgency=low * New upstream release correcting multiple bugs, changing the stats output, allowing optional scaffolding and multiple rounds of Pebble. * Added the programs velveth_de and velvetg_de to the package in /usr/bin, and the scripts shuffleSequences_fasta.pl and shuffleSequences_fastq.pl in /usr/share/velvet (debian/rules, debian/install). * Refreshed debian/copyright. * Temporarly disabled the manpage generation of velvetg* because the --help option is not available (debian/rules). -- Charles Plessy Tue, 09 Jun 2009 21:28:03 +0900 velvet (0.7.31-1) unstable; urgency=low * New upstream version * Standards-Version: 3.8.1 (no changes needed) * Create manpages using help2man * Move third-party/layout and third-party/afg_handling to examples because these scripts are actually not to run velvet but for the convenience of users - in /urs/share/velvet these scripts seem to be perfectly hidden and in /usr/share/doc/velvet might create users attendance * Added missing quilt entry in debian/rules -- Andreas Tille Fri, 27 Mar 2009 13:23:32 +0100 velvet (0.7.24-1) unstable; urgency=low * Initial release (Closes: #487026) -- Charles Plessy Wed, 09 Jul 2008 14:06:55 +0900 debian/patches/0000755000000000000000000000000012176652361010626 5ustar debian/patches/include_debians_zlib.patch0000644000000000000000000000162612022362113015763 0ustar Description: Use the zlib distributed by Debian, not the one in third-party/zlib-1.2.3/. Author: Charles Plessy Forwarded: no --- a/src/readSet.c +++ b/src/readSet.c @@ -39,7 +39,7 @@ Copyright 2007, 2008 Daniel Zerbino (zer #elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" #else -#include "../third-party/zlib-1.2.3/zlib.h" +#include #endif #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) --- a/src/binarySequences.c +++ b/src/binarySequences.c @@ -34,7 +34,7 @@ Copyright 2011 Convey Computer Corporati #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32) #include "../third-party/zlib-1.2.3/Win32/include/zlib.h" #else -#include "../third-party/zlib-1.2.3/zlib.h" +#include #endif #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__) debian/patches/fix-perl-path.patch0000644000000000000000000000051311620755351014322 0ustar Description: s?/usr/local/perl?/usr/perl? Author: Andreas Tille Forwarded: No --- a/contrib/select_paired/select_paired.pl +++ b/contrib/select_paired/select_paired.pl @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/perl -w # Konrad Paszkiewicz, University of Exeter UK. # k.h.paszkiewicz@exeter.ac.uk debian/patches/shuffleSequences_fasta.patch0000644000000000000000000000054311620755351016333 0ustar Description: Scripts need to specify interpreter in the first line Author: Andreas Tille Forwarded: not yet --- a/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py +++ b/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py @@ -1,3 +1,4 @@ +#!/usr/bin/python import sys from Bio import SeqIO def interleave(iter1, iter2) : debian/patches/series0000644000000000000000000000011411620755351012033 0ustar include_debians_zlib.patch shuffleSequences_fasta.patch fix-perl-path.patch debian/velvet.docs0000644000000000000000000000004212022364711011337 0ustar CREDITS.txt README.txt Manual.pdf debian/velvet.install0000644000000000000000000000002012176657630012070 0ustar velvet* usr/bin debian/velvet-example.install0000644000000000000000000000010212176657747013533 0ustar contrib usr/share/doc/velvet data/* usr/share/doc/velvet/examples debian/compat0000644000000000000000000000000212022371204010355 0ustar 9 debian/docs0000644000000000000000000000004211711104602010026 0ustar CREDITS.txt README.txt Manual.pdf