Author: tille Date: 2011-11-18 22:56:53 +0000 (Fri, 18 Nov 2011) New Revision: 8610
Added: trunk/packages/trimmomatic/ trunk/packages/trimmomatic/trunk/ trunk/packages/trimmomatic/trunk/debian/ trunk/packages/trimmomatic/trunk/debian/bin/ trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE trunk/packages/trimmomatic/trunk/debian/changelog trunk/packages/trimmomatic/trunk/debian/compat trunk/packages/trimmomatic/trunk/debian/control trunk/packages/trimmomatic/trunk/debian/copyright trunk/packages/trimmomatic/trunk/debian/install trunk/packages/trimmomatic/trunk/debian/rules trunk/packages/trimmomatic/trunk/debian/source/ trunk/packages/trimmomatic/trunk/debian/source/format trunk/packages/trimmomatic/trunk/debian/watch Modified: trunk/packages/libg2/trunk/debian/changelog Log: Inject trimmomatic (not finished) Modified: trunk/packages/libg2/trunk/debian/changelog =================================================================== --- trunk/packages/libg2/trunk/debian/changelog 2011-11-18 19:47:52 UTC (rev 8609) +++ trunk/packages/libg2/trunk/debian/changelog 2011-11-18 22:56:53 UTC (rev 8610) @@ -14,6 +14,16 @@ -- Andreas Tille <[email protected]> Fri, 04 Nov 2011 22:30:26 +0100 +g2 (0.72-2.1) unstable; urgency=low + + * Non-maintainer upload. + * Don't mix source format 3.0 (quilt) and manual usage of quilt: + - Drop manual quilt calls from debian/rules; + - Drop superfluous quilt Build-Depends. + Closes: #643478 + + -- Didier Raboud <[email protected]> Tue, 15 Nov 2011 16:59:33 +0100 + g2 (0.72-2) unstable; urgency=low * Took over package in Debian Med team maintenance Added: trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE =================================================================== --- trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticPE 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1,10 @@ +#!/bin/sh +PKGNAME=trimmomatic +FUNCNAME=`basename $0` +JARDIR=/usr/share/java +JARVERSION=`ls $JARDIR/$PKGNAME-*.jar | sort | tail -n 1` +if [ "" = "$JARVERSION" ] ; then + echo "Broken installation of $PKGNAME. JAR not found." + exit 1 +fi +java -classpath /usr/share/java/$JARVERSION org.usadellab.$PKGNAME.$FUNCNAME $@ Added: trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE =================================================================== --- trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1 @@ +link TrimmomaticPE \ No newline at end of file Property changes on: trunk/packages/trimmomatic/trunk/debian/bin/TrimmomaticSE ___________________________________________________________________ Added: svn:special + * Added: trunk/packages/trimmomatic/trunk/debian/changelog =================================================================== --- trunk/packages/trimmomatic/trunk/debian/changelog (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/changelog 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1,5 @@ +trimmomatic (0.17-1) unstable; urgency=low + + * Initial release (Closes: #?????) + + -- Andreas Tille <[email protected]> Fri, 18 Nov 2011 19:12:40 +0100 Added: trunk/packages/trimmomatic/trunk/debian/compat =================================================================== --- trunk/packages/trimmomatic/trunk/debian/compat (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/compat 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1 @@ +8 Added: trunk/packages/trimmomatic/trunk/debian/control =================================================================== --- trunk/packages/trimmomatic/trunk/debian/control (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/control 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1,37 @@ +Source: trimmomatic +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 8), javahelper +Standards-Version: 3.9.2 +Homepage: http://www.usadellab.org/cms/index.php?page=trimmomatic +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/trimmomatic/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/trimmomatic/trunk/ + +Package: trimmomatic +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: flexible read trimming tool for Illumina NGS data + Trimmomatic performs a variety of useful trimming tasks for illumina + paired-end and single ended data.The selection of trimming steps and + their associated parameters are supplied on the command line. + . + The current trimming steps are: + * ILLUMINACLIP: Cut adapter and other illumina-specific sequences from + the read. + * SLIDINGWINDOW: Perform a sliding window trimming, cutting once thes + average quality within the window falls below a threshold. + * LEADING: Cut bases off the start of a read, if below a threshold quality + * TRAILING: Cut bases off the end of a read, if below a threshold quality + * CROP: Cut the read to a specified length + * HEADCROP: Cut the specified number of bases from the start of the read + * MINLENGTH: Drop the read if it is below a specified length + * TOPHRED33: Convert quality scores to Phred-33 + * TOPHRED64: Convert quality scores to Phred-64 + It works with FASTQ (using phred + 33 or phred + 64 quality scores, + depending on the Illumina pipeline used), either uncompressed or + gzipp'ed FASTQ. Use of gzip format is determined based on the .gz + extension. + Added: trunk/packages/trimmomatic/trunk/debian/copyright =================================================================== --- trunk/packages/trimmomatic/trunk/debian/copyright (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/copyright 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1,28 @@ +Format: http://dep.debian.net/deps/dep5/ +Upstream-Name: Trimmomatic +Upstream-Contact: Bjoern Usadel <[email protected]> +Source: http://www.usadellab.org/cms/index.php?page=trimmomatic + +Files: * +Copyright: © 2009-2011 Bjoern Usadel <[email protected]>, + Anthony Bolger <[email protected]> +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 <http://www.gnu.org/licenses/>. +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: © 2011, Andreas Tille <[email protected]> +License: GPL-3+ + Same as package itself Added: trunk/packages/trimmomatic/trunk/debian/install =================================================================== --- trunk/packages/trimmomatic/trunk/debian/install (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/install 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1,2 @@ +dist/jar/*.jar usr/share/java + Added: trunk/packages/trimmomatic/trunk/debian/rules =================================================================== --- trunk/packages/trimmomatic/trunk/debian/rules (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/rules 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1,11 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules file for beast-mcmc +# Andreas Tille <[email protected]> +# GPL + +%: + dh $@ --with javahelper + +get-orig-source: + uscan --verbose --force-download --repack --rename Property changes on: trunk/packages/trimmomatic/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/trimmomatic/trunk/debian/source/format =================================================================== --- trunk/packages/trimmomatic/trunk/debian/source/format (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/source/format 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/trimmomatic/trunk/debian/watch =================================================================== --- trunk/packages/trimmomatic/trunk/debian/watch (rev 0) +++ trunk/packages/trimmomatic/trunk/debian/watch 2011-11-18 22:56:53 UTC (rev 8610) @@ -0,0 +1,3 @@ +version=3 +http://www.usadellab.org/cms/index.php?page=trimmomatic \ + uploads/supplementary/Trimmomatic/Trimmomatic-Src-([.\d]*).zip _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
