Author: tille Date: 2011-03-18 18:47:31 +0000 (Fri, 18 Mar 2011) New Revision: 6296
Added: trunk/packages/abacas/trunk/debian/abacas.1 trunk/packages/abacas/trunk/debian/get-orig-source trunk/packages/abacas/trunk/debian/install trunk/packages/abacas/trunk/debian/manpages trunk/packages/abacas/trunk/debian/rules Modified: trunk/packages/abacas/trunk/debian/changelog trunk/packages/abacas/trunk/debian/compat trunk/packages/abacas/trunk/debian/control trunk/packages/abacas/trunk/debian/watch Log: Manpage, rules, get-orig-source Added: trunk/packages/abacas/trunk/debian/abacas.1 =================================================================== --- trunk/packages/abacas/trunk/debian/abacas.1 (rev 0) +++ trunk/packages/abacas/trunk/debian/abacas.1 2011-03-18 18:47:31 UTC (rev 6296) @@ -0,0 +1,104 @@ +.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 <[email protected]>, +for the Debian project (and may be used by others). Modified: trunk/packages/abacas/trunk/debian/changelog =================================================================== --- trunk/packages/abacas/trunk/debian/changelog 2011-03-18 17:26:52 UTC (rev 6295) +++ trunk/packages/abacas/trunk/debian/changelog 2011-03-18 18:47:31 UTC (rev 6296) @@ -1,6 +1,5 @@ abacas (1.3.1-1) unstable; urgency=low * Initial release (Closes: #????) - PACKAGING NOT FINISHED - FEEL FREE TO TAKE OVER - -- Andreas Tille <[email protected]> Mon, 11 Feb 2011 12:02:43 +0100 + -- Andreas Tille <[email protected]> Mon, 07 Feb 2011 12:02:43 +0100 Modified: trunk/packages/abacas/trunk/debian/compat =================================================================== --- trunk/packages/abacas/trunk/debian/compat 2011-03-18 17:26:52 UTC (rev 6295) +++ trunk/packages/abacas/trunk/debian/compat 2011-03-18 18:47:31 UTC (rev 6296) @@ -1 +1 @@ -7 +8 Modified: trunk/packages/abacas/trunk/debian/control =================================================================== --- trunk/packages/abacas/trunk/debian/control 2011-03-18 17:26:52 UTC (rev 6295) +++ trunk/packages/abacas/trunk/debian/control 2011-03-18 18:47:31 UTC (rev 6296) @@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7.1) +Build-Depends: debhelper (>= 8) Standards-Version: 3.9.1 Homepage: http://abacas.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/abacas/trunk/?rev=0&sc=0 Added: trunk/packages/abacas/trunk/debian/get-orig-source =================================================================== --- trunk/packages/abacas/trunk/debian/get-orig-source (rev 0) +++ trunk/packages/abacas/trunk/debian/get-orig-source 2011-03-18 18:47:31 UTC (rev 6296) @@ -0,0 +1,38 @@ +#!/bin/sh +# 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 \([0-9.]\+\) .*download.html.*?\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}.${VERSION}.pl + +GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "$PKG"-"$VERSION" +rm -rf "$PKG"-"$VERSION" Added: trunk/packages/abacas/trunk/debian/install =================================================================== --- trunk/packages/abacas/trunk/debian/install (rev 0) +++ trunk/packages/abacas/trunk/debian/install 2011-03-18 18:47:31 UTC (rev 6296) @@ -0,0 +1 @@ +abacas usr/bin Added: trunk/packages/abacas/trunk/debian/manpages =================================================================== --- trunk/packages/abacas/trunk/debian/manpages (rev 0) +++ trunk/packages/abacas/trunk/debian/manpages 2011-03-18 18:47:31 UTC (rev 6296) @@ -0,0 +1 @@ +debian/*.1 Added: trunk/packages/abacas/trunk/debian/rules =================================================================== --- trunk/packages/abacas/trunk/debian/rules (rev 0) +++ trunk/packages/abacas/trunk/debian/rules 2011-03-18 18:47:31 UTC (rev 6296) @@ -0,0 +1,11 @@ +#!/usr/bin/make -f +# debian/rules for abacas +# Andreas Tille <[email protected]> +# GPL + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ + Property changes on: trunk/packages/abacas/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Modified: trunk/packages/abacas/trunk/debian/watch =================================================================== --- trunk/packages/abacas/trunk/debian/watch 2011-03-18 17:26:52 UTC (rev 6295) +++ trunk/packages/abacas/trunk/debian/watch 2011-03-18 18:47:31 UTC (rev 6296) @@ -1,2 +1,3 @@ version=3 -http://sf.net/abacas/abacas\.([\d\.]+)\.pl +http://sf.net/abacas/abacas\.([\d\.]+)\.pl \ + debian debian/get-orig-source _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
