debian/0000755000000000000000000000000012232475146007174 5ustar debian/control0000644000000000000000000000263412232474613010602 0ustar Source: abacas Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/abacas/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/abacas/trunk/ Homepage: http://abacas.sourceforge.net/ Package: abacas Architecture: all Depends: ${perl:Depends}, ${misc:Depends}, mummer Description: Algorithm Based Automatic Contiguation of Assembled Sequences ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. . ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then processed to generate a pseudomolecule taking overlapping contigs and gaps in to account. ABACAS generates a comparision file that can be used to visualize ordered and oriented contigs in ACT. Synteny is represented by red bars where colour intensity decreases with lower values of percent identity between comparable blocks. Information on contigs such as the orientation, percent identity, coverage and overlap with other contigs can also be visualized by loading the outputted feature file on ACT. debian/install0000644000000000000000000000001711540676346010571 0ustar abacas usr/bin debian/abacas.10000644000000000000000000000533411540705636010476 0ustar .TH ABACAS "1" "2011-02-11" "1.3.1" "User Commands" .SH NAME abacas \- Algorithm Based Automatic Contiguation of Assembled Sequences .SH SYNOPSIS .B abacas \fB\-r\fR \fIref\fR \fB\-q\fR \fIqs\fR \fB\-p\fR \fIprog\fR [OPTIONS] .PP OR .PP .B abacas \fB\-r\fR \fIref\fR \fB\-q\fR \fIpsf\fR \fB\-e\fR .PP .TP \fIref\fR reference sequence in a single fasta file .TP \fIqs\fR contigs in multi\-fasta format .TP \fI\prog\fR MUMmer program to use: 'nucmer' or 'promer' .TP \fIpsf\fR pseudomolecule/ordered sequence file in fasta format .PP \fBOPTIONS\fR .TP \fB\-h\fR print usage .TP \fB\-d\fR use default nucmer/promer parameters .TP \fB\-s\fR int minimum length of exact matching word (nucmer default = 12, promer default = 4) .TP \fB\-m\fR print ordered contigs to file in multifasta format .TP \fB\-b\fR print contigs in bin to file .TP \fB\-N\fR print a pseudomolecule without "N"s .TP \fB\-i\fR int mimimum percent identity [default 40] .TP \fB\-v\fR int mimimum contig coverage [default 40] .TP \fB\-V\fR int minimum contig coverage difference [default 1] .TP \fB\-l\fR int minimum contig length [default 1] .TP \fB\-t\fR run tblastx on contigs that are not mapped .TP \fB\-g\fR string (file name) print uncovered regions (gaps) on reference to file name .TP \fB\-a\fR append contigs in bin to the pseudomolecule .TP \fB\-o\fR prefix output files will have this prefix .TP \fB\-P\fR pick primer sets to close gaps .TP \fB\-f\fR int number of flanking bases on either side of a gap for primer design (default 350) .TP \fB\-R\fR int Run mummer [default 1, use \fB\-R\fR 0 to avoid running mummer] .TP \fB\-e\fR Escape contig ordering i.e. go to primer design .TP \fB\-c\fR Reference sequence is circular .SH DESCRIPTION ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. .PP ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then processed to generate a pseudomolecule taking overlapping contigs and gaps in to account. ABACAS generates a comparision file that can be used to visualize ordered and oriented contigs in ACT. Synteny is represented by red bars where colour intensity decreases with lower values of percent identity between comparable blocks. Information on contigs such as the orientation, percent identity, coverage and overlap with other contigs can also be visualized by loading the outputted feature file on ACT. .SH AUTHOR ABACAS IS Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK. .PP This manual page was written by Andreas Tille , for the Debian project (and may be used by others). debian/rules0000755000000000000000000000031511541611046010244 0ustar #!/usr/bin/make -f # debian/rules for abacas # Andreas Tille # GPL # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ get-orig-source: . debian/get-orig-source debian/manpages0000644000000000000000000000001311540705460010700 0ustar debian/*.1 debian/watch0000644000000000000000000000012611540671573010227 0ustar version=3 http://sf.net/abacas/abacas\.([\d\.]+)\.pl \ debian debian/get-orig-source debian/upstream0000644000000000000000000000074312214301212010741 0ustar Reference: Author: Samuel Assefa and Thomas M. Keane and Thomas D. Otto and Chris Newbold and Matthew Berriman Title: "ABACAS: algorithm-based automatic contiguation of assembled sequences" Journal: Bioinformatics Year: 2009 Volume: 25 Number: 15 Pages: 1968-1969 DOI: 10.1093/bioinformatics/btp347 PMID: 19497936 URL: http://bioinformatics.oxfordjournals.org/content/25/15/1968 eprint: http://bioinformatics.oxfordjournals.org/content/25/15/1968.full.pdf+html debian/copyright0000644000000000000000000000232112232474770011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Abacas Upstream-Contact: Wellcome Trust Sanger Institute Source: http://sourceforge.net/projects/abacas/files/ Files: * Copyright: © 2008-10 Genome Research Limited. All Rights Reserved. License: GPL-2+ Files: debian/* Copyright: © 2011 Andreas Tille License: GPL-2+ License: GPL-2+ Abacas 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 . 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/0000755000000000000000000000000011525236732010474 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/get-orig-source0000755000000000000000000000333511541612044012131 0ustar #!/bin/sh -e # creating source tarbal for abacas which comes as plain Perl file # and needs to be putin to a tarball PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` if ! echo $@ | grep -q upstream-version ; then # if called manually run uscan to obtain file and version number # VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` 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/"` else # If called by uscan VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\) .*abacas.*?\1?'` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi #if [ "$VERSION" = "" ] ; then # VERSION=`ls ../${PKG}.*.pl | sed "s/.*$PKG\.\(.*\)\.pl/\1/"` #fi mkdir -p ../tarballs/${PKG}-${VERSION} cd ../tarballs # Rename perl file (without .pl suffix) and fix perl path sed -e '1s?/usr/local/bin/perl?/usr/bin/perl?' \ -e "s/^${PKG}.pl/${PKG}/" \ ../${PKG}.${VERSION}.pl > ${PKG}-${VERSION}/${PKG} touch -r ../${PKG}.${VERSION}.pl ${PKG}-${VERSION}/${PKG} rm -f ../${PKG}.${VERSION}.pl cd ${PKG}-${VERSION} wget -q -N http://abacas.sourceforge.net/Manual.html sed -i -e 's?index.html">Home?http://abacas.sourceforge.net/&?' \ -e 's?documentation.html">Documentation?http://abacas.sourceforge.net/&?' \ -e 's/perl abacas\.pl/abacas/' \ -e 's/abacas\.pl/abacas/' \ Manual.html wget -q -N http://abacas.sourceforge.net/style.css cd .. GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "$PKG"-"$VERSION" rm -rf "$PKG"-"$VERSION" debian/changelog0000644000000000000000000000065412232475146011053 0ustar abacas (1.3.1-2) unstable; urgency=low * debian/upstream: Added citation information * debian/control: - cme fix dpkg-control - debhelper 9 - canocoal Vcs URLs * debian/copyright: DEP5 -- Andreas Tille Fri, 25 Oct 2013 15:59:00 +0200 abacas (1.3.1-1) unstable; urgency=low * Initial release (Closes: #619100) -- Andreas Tille Mon, 21 Mar 2011 09:48:04 +0100 debian/doc-base0000644000000000000000000000070211542326277010576 0ustar Document: abacas Title: Abacas user manual Author: Wellcome Trust Sanger Institute Abstract: Algorithm Based Automatic Contiguation of Assembled Sequences ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. Section: Science/Biology Format: html Files: /usr/share/doc/abacas/Manual.html Index: /usr/share/doc/abacas/Manual.html debian/compat0000644000000000000000000000000212232474541010370 0ustar 9 debian/docs0000644000000000000000000000001511541610202010025 0ustar *.html *.css