[med-svn] r12803 - in trunk/packages: . beast-mcmc/trunk/debian/patches flexbar flexbar/trunk flexbar/trunk/debian flexbar/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Fri Jan 18 15:06:23 UTC 2013
Author: tille
Date: 2013-01-18 15:06:22 +0000 (Fri, 18 Jan 2013)
New Revision: 12803
Added:
trunk/packages/flexbar/
trunk/packages/flexbar/trunk/
trunk/packages/flexbar/trunk/debian/
trunk/packages/flexbar/trunk/debian/changelog
trunk/packages/flexbar/trunk/debian/compat
trunk/packages/flexbar/trunk/debian/control
trunk/packages/flexbar/trunk/debian/copyright
trunk/packages/flexbar/trunk/debian/rules
trunk/packages/flexbar/trunk/debian/source/
trunk/packages/flexbar/trunk/debian/source/format
trunk/packages/flexbar/trunk/debian/upstream
trunk/packages/flexbar/trunk/debian/watch
Modified:
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
Log:
Initial kickstart for flexbar
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2013-01-18 14:24:11 UTC (rev 12802)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2013-01-18 15:06:22 UTC (rev 12803)
@@ -2,8 +2,65 @@
Date: Tue, 10 Jan 2012 22:29:24 +0100
Description: Make sure package builds with Debian packages JARs
---- beast-mcmc-1.7.2.orig/.classpath
-+++ beast-mcmc-1.7.2/.classpath
+--- beast-mcmc-1.6.2.orig/build.xml
++++ beast-mcmc-1.6.2/build.xml
+@@ -9,6 +9,7 @@
+ <property name="src" location="src" />
+ <property name="build" location="build" />
+ <property name="lib" location="lib" />
++ <property name="deblib" location="/usr/share/java" />
+ <property name="dist" location="${build}/dist" />
+
+ <property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
+@@ -20,6 +21,19 @@
+
+ <path id="classpath">
+ <fileset dir="${lib}" includes="**/*.jar"/>
++ <fileset dir="${deblib}" includes="beagle.jar"/>
++ <fileset dir="${deblib}" includes="colt.jar"/>
++ <fileset dir="${deblib}" includes="commons-math.jar"/>
++ <fileset dir="${deblib}" includes="figtree.jar"/>
++ <fileset dir="${deblib}" includes="itext1.jar"/>
++ <fileset dir="${deblib}" includes="jam.jar"/>
++ <fileset dir="${deblib}" includes="jdom1.jar"/>
++ <fileset dir="${deblib}" includes="jebl.jar"/>
++ <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/>
++ <fileset dir="${deblib}" includes="junit4.jar"/>
++ <fileset dir="${deblib}" includes="mpj.jar"/>
++ <fileset dir="${deblib}" includes="mtj.jar"/>
++ <fileset dir="${deblib}" includes="options.jar"/>
+ </path>
+
+ <!-- start -->
+@@ -130,14 +144,6 @@
+ <include name="org/virion/jam/**/*.png" />
+ <include name="dr/**/*.properties" />
+ </fileset>
+- <zipgroupfileset dir="${lib}" includes="jebl.jar" />
+- <zipgroupfileset dir="${lib}" includes="jam.jar" />
+- <zipgroupfileset dir="${lib}" includes="jdom.jar" />
+- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" />
+- <zipgroupfileset dir="${lib}" includes="mtj.jar" />
+- <zipgroupfileset dir="${lib}" includes="JRI.jar" />
+- <zipgroupfileset dir="${lib}" includes="colt.jar" />
+- <zipgroupfileset dir="${lib}" includes="beagle.jar" />
+ </jar>
+
+ <!-- Put everything in ${build} into the beauti.jar file -->
+@@ -193,11 +199,6 @@
+ <fileset dir="${src}">
+ <include name="dr/**/*.png" />
+ </fileset>
+- <zipgroupfileset dir="${lib}" includes="jam.jar" />
+- <zipgroupfileset dir="${lib}" includes="jebl.jar" />
+- <zipgroupfileset dir="${lib}" includes="jdom.jar" />
+- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" />
+- <zipgroupfileset dir="${lib}" includes="mtj.jar" />
+ </jar>
+
+ <!-- <jar jarfile="${dist}/treestat.jar">
+--- beast-mcmc-1.6.2.orig/.classpath
++++ beast-mcmc-1.6.2/.classpath
@@ -1,20 +1,20 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
@@ -17,82 +74,24 @@
- <classpathentry kind="lib" path="lib/jebl.jar"/>
- <classpathentry kind="lib" path="lib/JRI.jar"/>
- <classpathentry kind="lib" path="lib/junit-4.4.jar"/>
-- <classpathentry kind="lib" path="lib/libjri.jnilib"/>
- <classpathentry kind="lib" path="lib/mpj.jar"/>
- <classpathentry kind="lib" path="lib/mtj.jar"/>
- <classpathentry kind="lib" path="lib/options.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/beagle.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/colt.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/figtreepanel.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/itext-1.4.5.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/figtree.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/itext1.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jam.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/jdom.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/jdom1.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/JRI.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/junit-4.4.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/libjri.jnilib"/>
++ <classpathentry kind="lib" path="/usr/lib/R/site-library/rJava/jri/JRI.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/junit4.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/mpj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/mtj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/options.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-- <classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/commons-math-2.2.jar"/>
+- <classpathentry kind="lib" path="lib/commons-math-2.0.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
+ <classpathentry kind="lib" path="lib/libjri.jnilib"/>
<classpathentry kind="output" path="bin"/>
</classpath>
---- beast-mcmc-1.7.2.orig/build.xml
-+++ beast-mcmc-1.7.2/build.xml
-@@ -9,6 +9,7 @@
- <property name="src" location="src"/>
- <property name="build" location="build"/>
- <property name="lib" location="lib"/>
-+ <property name="deblib" location="/usr/share/java" />
- <property name="dist" location="${build}/dist"/>
-
- <property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
-@@ -21,6 +22,19 @@
-
- <path id="classpath">
- <fileset dir="${lib}" includes="**/*.jar"/>
-+ <fileset dir="${deblib}" includes="beagle.jar"/>
-+ <fileset dir="${deblib}" includes="colt.jar"/>
-+ <fileset dir="${deblib}" includes="commons-math.jar"/>
-+ <fileset dir="${deblib}" includes="figtree.jar"/>
-+ <fileset dir="${deblib}" includes="itext1.jar"/>
-+ <fileset dir="${deblib}" includes="jam.jar"/>
-+ <fileset dir="${deblib}" includes="jdom1.jar"/>
-+ <fileset dir="${deblib}" includes="jebl.jar"/>
-+ <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/>
-+ <fileset dir="${deblib}" includes="junit4.jar"/>
-+ <fileset dir="${deblib}" includes="mpj.jar"/>
-+ <fileset dir="${deblib}" includes="mtj.jar"/>
-+ <fileset dir="${deblib}" includes="options.jar"/>
- </path>
-
- <!-- start -->
-@@ -132,14 +146,6 @@
- <include name="org/virion/jam/**/*.png"/>
- <include name="dr/**/*.properties"/>
- </fileset>
-- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jdom.jar"/>
-- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
-- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
-- <zipgroupfileset dir="${lib}" includes="JRI.jar"/>
-- <zipgroupfileset dir="${lib}" includes="colt.jar"/>
-- <zipgroupfileset dir="${lib}" includes="beagle.jar"/>
- </jar>
-
- <!-- Put everything in ${build} into the beauti.jar file -->
-@@ -195,11 +201,6 @@
- <fileset dir="${src}">
- <include name="dr/**/*.png"/>
- </fileset>
-- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
-- <zipgroupfileset dir="${lib}" includes="jdom.jar"/>
-- <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
-- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
- </jar>
-
- </target>
Added: trunk/packages/flexbar/trunk/debian/changelog
===================================================================
--- trunk/packages/flexbar/trunk/debian/changelog (rev 0)
+++ trunk/packages/flexbar/trunk/debian/changelog 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1,5 @@
+flexbar (2.31-1) unstable; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- DMPT <debian-med-packaging at lists.alioth.debian.org> Thu, 24 May 2012 14:30:13 +0200
Added: trunk/packages/flexbar/trunk/debian/compat
===================================================================
--- trunk/packages/flexbar/trunk/debian/compat (rev 0)
+++ trunk/packages/flexbar/trunk/debian/compat 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1 @@
+9
Added: trunk/packages/flexbar/trunk/debian/control
===================================================================
--- trunk/packages/flexbar/trunk/debian/control (rev 0)
+++ trunk/packages/flexbar/trunk/debian/control 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1,26 @@
+Source: flexbar
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.4
+Homepage: https://sourceforge.net/projects/flexbar/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/flexbar/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/flexbar/trunk/
+
+Package: flexbar
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: flexible barcode and adapter removal for sequencing platforms
+ Flexbar preprocesses high-throughput sequencing data efficiently. It
+ demultiplexes barcoded runs and removes adapter sequences. Moreover,
+ trimming and filtering features are provided. Flexbar increases mapping
+ rates and improves genome and transcriptome assemblies. It supports
+ next-generation sequencing data in fasta/q and csfasta/q format from
+ Illumina, Roche 454, and the SOLiD platform.
+ .
+ Parameter names changed in Flexbar. Please review scripts. The recent
+ months, default settings were optimised, several bugs were fixed and
+ various improvements were made, e.g. revamped command-line interface,
+ new trimming modes as well as lower time and memory requirements.
Added: trunk/packages/flexbar/trunk/debian/copyright
===================================================================
--- trunk/packages/flexbar/trunk/debian/copyright (rev 0)
+++ trunk/packages/flexbar/trunk/debian/copyright 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Flexbar
+Source: https://sourceforge.net/projects/flexbar/files/
+
+Files: *
+Copyright: © 2012-2013 Matthias Dodt <matthias.dodt at googlemail.com>
+ Johannes T. Roehremail <johannes.roehr at mdc-berlin.de>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: © 2013 Andreas Tille <tille at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ 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 package 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/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
Added: trunk/packages/flexbar/trunk/debian/rules
===================================================================
--- trunk/packages/flexbar/trunk/debian/rules (rev 0)
+++ trunk/packages/flexbar/trunk/debian/rules 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
Property changes on: trunk/packages/flexbar/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/flexbar/trunk/debian/source/format
===================================================================
--- trunk/packages/flexbar/trunk/debian/source/format (rev 0)
+++ trunk/packages/flexbar/trunk/debian/source/format 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/flexbar/trunk/debian/upstream
===================================================================
--- trunk/packages/flexbar/trunk/debian/upstream (rev 0)
+++ trunk/packages/flexbar/trunk/debian/upstream 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1,11 @@
+Reference:
+ Author: Matthias Dodt and Johannes T. Roehr and Rina Ahmed and Christoph Dieterich
+ Title: "FLEXBAR — Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms"
+ Journal: Biology
+ Year: 2012
+ Volume: 1
+ Number: 3
+ Pages: 895-905
+ DOI: 10.3390/biology1030895
+ URL: http://www.mdpi.com/2079-7737/1/3/895
+ eprint: http://www.mdpi.com/2079-7737/1/3/895/pdf
Added: trunk/packages/flexbar/trunk/debian/watch
===================================================================
--- trunk/packages/flexbar/trunk/debian/watch (rev 0)
+++ trunk/packages/flexbar/trunk/debian/watch 2013-01-18 15:06:22 UTC (rev 12803)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/flexbar/flexbar-(.*)\.tar\.gz
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