[med-svn] [ipig] 01/01: Add initial Debian packaging
Andreas Tille
tille at debian.org
Sat Feb 8 21:17:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ipig.
commit f5b88b4ccc1f05a62b1ef994e2de3b29c6789b1c
Author: Andreas Tille <tille at debian.org>
Date: Sat Feb 8 22:17:12 2014 +0100
Add initial Debian packaging
---
debian/build.xml | 52 ++++++++++++++++++++++++++++++++++++++++++++++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 31 ++++++++++++++++++++++++++++++
debian/copyright | 36 ++++++++++++++++++++++++++++++++++
debian/get-orig-source | 31 ++++++++++++++++++++++++++++++
debian/rules | 23 ++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream | 12 ++++++++++++
debian/watch | 4 ++++
10 files changed, 196 insertions(+)
diff --git a/debian/build.xml b/debian/build.xml
new file mode 100644
index 0000000..2bf37c0
--- /dev/null
+++ b/debian/build.xml
@@ -0,0 +1,52 @@
+<?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>
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..61aa118
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+ipig (0.0.r5-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Sat, 08 Feb 2014 08:47:28 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..c450a5e
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,31 @@
+Source: ipig
+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),
+ 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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..fcd466a
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,36 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: iPiG
+Upstream-Contact: Mathias Kuhring <KuhringM at rki.de>
+Source: http://sourceforge.net/projects/ipig/files/
+
+Files: *
+Copyright: 2012-2013 Mathias Kuhring <KuhringM at rki.de>
+ Robert Koch-Institut
+License: BSDlike
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at 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.
+
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..1c33f8a
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,31 @@
+#!/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 ${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..387628d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+SRC_VERSION =$(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
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream b/debian/upstream
new file mode 100644
index 0000000..d1d8ed7
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,12 @@
+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
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..feb8aa3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+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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