Commit f5b88b4c authored by Andreas Tille's avatar Andreas Tille

Add initial Debian packaging

parent cb38fe49
<?xml version="1.0" ?>
<project name="iPiG" default="jar" basedir=".">
<!-- Directory structure -->
<property name="build.dir" location="build"/>
<property name="dist.dir" location="dist"/>
<property name="src.dir" location="src"/>
<property name="lib.dir" location="/usr/share/java"/>
<property name="class.dir" location="${build.dir}/classes"/>
<property name="project.name" value="ipig"/>
<property name="debug" value="true"/>
<property name="optimized" value="true"/>
<property name="project.version" value="DEBVERSION"/>
<property environment="env"/>
<property name="project.jarfile.name" value="iPiG.jar"/>
<property name="class.path" value=""/>
<path id="compile.classpath">
<fileset dir="${lib.dir}">
</fileset>
</path>
<target name="clean">
<echo level="info">Cleaning build directories</echo>
<delete verbose="true" includeEmptyDirs="true">
<fileset dir="${build.dir}" includes="**"/>
<fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
</delete>
</target>
<target name="compile">
<mkdir dir="${class.dir}"/>
<mkdir dir="${dist.dir}"/>
<javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
</javac>
</target>
<target name="jar" depends="compile">
<jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
<manifest>
<attribute name="Built-By" value="Debian-Med team"/>
<attribute name="Main-Class" value="de.rki.ng4.ipig.Ipig"/>
<attribute name="Class-Path" value="${class.path}"/>
<attribute name="Specification-Title" value="iPiG"/>
<attribute name="Specification-Version" value="${project.version}"/>
</manifest>
</jar>
</target>
</project>
ipig (0.0.r5-1) UNRELEASED; urgency=low
* Initial release (Closes: #<bug>)
-- Andreas Tille <tille@debian.org> Sat, 08 Feb 2014 08:47:28 +0100
Source: ipig
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Build-Depends: debhelper (>= 9),
javahelper (>=0.25),
default-jdk,
ant,
libcommons-compress-java,
libcommons-net-java,
libjdom1-java,
libxerces2-java
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/ipig.git
Vcs-Git: git://anonscm.debian.org/debian-med/ipig.git
Homepage: http://sourceforge.net/projects/ipig/
Package: ipig
Architecture: any
Depends: ${misc:Depends},
${java:Depends},
Description: Integrating PSMs into Genome browser visualisations
iPiG targets the integration of peptide spectrum matches (PSMs) from
mass spectrometry (MS) peptide identifications into genomic
visualisations provided by genome browser such as the UCSC genome
browser (http://genome.ucsc.edu/).
.
iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in
text format and provides results in genome track formats (BED and GFF3
files), which can be easily imported into genome browsers.
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: iPiG
Upstream-Contact: Mathias Kuhring <KuhringM@rki.de>
Source: http://sourceforge.net/projects/ipig/files/
Files: *
Copyright: 2012-2013 Mathias Kuhring <KuhringM@rki.de>
Robert Koch-Institut
License: BSDlike
Files: debian/*
Copyright: 2014 Andreas Tille <tille@debian.org>
License: BSDlike
License: BSDlike
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* The name of the author may not be used to endorse or promote products
derived from this software without specific prior written permission.
.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL MARTIN S. LINDNER BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#!/bin/sh
# get source of iPiG from svn
COMPRESS=xz
set -e
NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
if ! echo $@ | grep -q upstream-version ; then
VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
else
VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
if echo "$VERSION" | grep -q "upstream-version" ; then
echo "Unable to parse version number"
exit
fi
fi
TARDIR=${NAME}-${VERSION}
mkdir -p ../tarballs
cd ../tarballs
# need to clean up the tarballs dir first because upstream tarball might
# contain a directory with unpredictable name
rm -rf *
# fetch source from SVN
svn export svn://svn.code.sf.net/p/ipig/code/trunk $TARDIR
rm -fr $TARDIR/lib/*.jar
GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
rm -rf ${TARDIR}
#!/usr/bin/make -f
# DH_VERBOSE := 1
SRC_VERSION =$(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
export JAVA_HOME=/usr/lib/jvm/default-java
%:
dh $@ --with javahelper
get-orig-source:
. debian/get-orig-source
override_dh_clean:
rm -f build.xml
dh_clean
override_dh_auto_build:
cp debian/build.xml build.xml
sed -i "s/DEBVERSION/"$(SRC_VERSION)"/g" build.xml
dh_auto_build
Reference:
Author: Mathias Kuhring and Bernhard Y. Renard
Title: "iPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations"
Journal: PLoS ONE
Year: 2012
Volume: 7
Number: 12
Pages: e50246
DOI: 10.1371/journal.pone.0050246
PMID: 23226516
URL: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050246
eprint: http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0050246&representation=PDF
version=3
opts=uversionmangle=s/^/0.0./ \
http://sf.net/ipig/ipig_(r[0-9]+)\.(?:tgz|tar\.gz|tar\.xz|tar\.bz2|zip) \
debian debian/get-orig-source
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