[med-svn] r8610 - in trunk/packages: . libg2/trunk/debian trimmomatic trimmomatic/trunk trimmomatic/trunk/debian trimmomatic/trunk/debian/bin trimmomatic/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Fri Nov 18 22:56:54 UTC 2011
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 <tille at debian.org> 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 <odyx at debian.org> 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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+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 <usadel at mpimp-golm.mpg.de>
+Source: http://www.usadellab.org/cms/index.php?page=trimmomatic
+
+Files: *
+Copyright: © 2009-2011 Bjoern Usadel <usadel at mpimp-golm.mpg.de>,
+ Anthony Bolger <Bolger at mpimp-golm.mpg.de>
+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 <tille at debian.org>
+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 <tille at debian.org>
+# 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
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