Author: tille Date: 2012-01-26 19:23:44 +0000 (Thu, 26 Jan 2012) New Revision: 9441
Added: trunk/packages/spread/trunk/debian/README.Debian trunk/packages/spread/trunk/debian/copyright trunk/packages/spread/trunk/debian/get-orig-source trunk/packages/spread/trunk/debian/install trunk/packages/spread/trunk/debian/manifest trunk/packages/spread/trunk/debian/patches/ trunk/packages/spread/trunk/debian/patches/build_xml.patch trunk/packages/spread/trunk/debian/patches/follow_hint_from_README.patch trunk/packages/spread/trunk/debian/patches/series trunk/packages/spread/trunk/debian/rules Modified: trunk/packages/spread/trunk/debian/changelog trunk/packages/spread/trunk/debian/control Log: Packaged Spread when travaling; Remark: I do not honestly want to Build-Depend from arduino package, but this package contains core.jar for the moment - will ask maintainer for a separate package to Build-Depend from Added: trunk/packages/spread/trunk/debian/README.Debian =================================================================== --- trunk/packages/spread/trunk/debian/README.Debian (rev 0) +++ trunk/packages/spread/trunk/debian/README.Debian 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,9 @@ +SPREAD for Debian +----------------- + +Please note: + + Originally this program is named "spread". However, there is just such a + package inside Debian and thus a 'phy-' for phylogeny was prepended. + + -- Andreas Tille <[email protected]> Thu, 26 Jan 2012 18:51:29 +0100 Modified: trunk/packages/spread/trunk/debian/changelog =================================================================== --- trunk/packages/spread/trunk/debian/changelog 2012-01-26 19:21:23 UTC (rev 9440) +++ trunk/packages/spread/trunk/debian/changelog 2012-01-26 19:23:44 UTC (rev 9441) @@ -2,4 +2,4 @@ * Initial release. (Closes: ) - -- Andreas Tille <[email protected]> Wed, 21 Dec 2011 09:18:47 +0100 + -- Andreas Tille <[email protected]> Thu, 26 Jan 2012 18:51:29 +0100 Modified: trunk/packages/spread/trunk/debian/control =================================================================== --- trunk/packages/spread/trunk/debian/control 2012-01-26 19:21:23 UTC (rev 9440) +++ trunk/packages/spread/trunk/debian/control 2012-01-26 19:23:44 UTC (rev 9441) @@ -5,7 +5,9 @@ DM-Upload-Allowed: yes Uploaders: Andreas Tille <[email protected]> Build-Depends: debhelper (>= 8), javahelper (>=0.25), - ant, ant-optional, openjdk-6-jdk | default-jdk + ant, ant-optional, openjdk-6-jdk | default-jdk, + libcolorpicker-java, libjebl2-java, libcolt-java, + arduino Standards-Version: 3.9.2 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phy-spread/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phy-spread/trunk/ @@ -14,7 +16,7 @@ Package: phy-spread Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, openjdk-6-jre | java-jre +Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, openjdk-6-jre | java-jre Description: analyze and visualize phylogeographic reconstructions SPREAD is a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of Added: trunk/packages/spread/trunk/debian/copyright =================================================================== --- trunk/packages/spread/trunk/debian/copyright (rev 0) +++ trunk/packages/spread/trunk/debian/copyright 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,31 @@ +Format: http://dep.debian.net/deps/dep5/ +Upstream-Name: Spread +Upstream-Contact: Filip Bielejec <[email protected]> +Original-Source: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html + +Copyright: 2004-2011 Filip Bielejec <[email protected]>, + Andrew Rambaut <[email protected]>, + Marc A. Suchard <[email protected]>, + Philippe Lemey +License: LGPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser 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 Lesser General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included + in the file ‘/usr/share/common-licenses/LGPL-3’, and the GNU GPL license + version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’. + +Files: debian/* +Copyright: © 2012 Andreas Tille <[email protected]> +License: LGPL-3+ + Same license as the software itself Added: trunk/packages/spread/trunk/debian/get-orig-source =================================================================== --- trunk/packages/spread/trunk/debian/get-orig-source (rev 0) +++ trunk/packages/spread/trunk/debian/get-orig-source 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,33 @@ +#!/bin/sh +# unpack spread tarball to get rid of several binaries + +set -e +NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +UPSTREAMNAME=`echo $NAME | sed 's/phy-//'` + +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 \([0-9.]\+\) .*${UPSTREAMNAME}.*?\1?"` + if echo "$VERSION" | grep -q "upstream-version" ; then + echo "Unable to parse version number" + exit + fi +fi + +TARDIR=${UPSTREAMNAME}-${VERSION} +mkdir -p ../tarballs +cd ../tarballs +mv ../${TARDIR}.tar.gz . +tar -xzf ${TARDIR}.tar.gz + +# Remove useless binaries +rm -rf ${TARDIR}/release/Mac +rm -rf ${TARDIR}/release/Windows +rm -rf ${TARDIR}/release/tools + +# Remove debian packaged jars +rm -rf ${TARDIR}/lib/* + +GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf "$NAME"_"$VERSION".orig.tar.gz "${TARDIR}" +rm -rf ${TARDIR} Property changes on: trunk/packages/spread/trunk/debian/get-orig-source ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/spread/trunk/debian/install =================================================================== --- trunk/packages/spread/trunk/debian/install (rev 0) +++ trunk/packages/spread/trunk/debian/install 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,2 @@ +dist/*.jar usr/share/java +debian/scripts/* usr/bin Added: trunk/packages/spread/trunk/debian/manifest =================================================================== --- trunk/packages/spread/trunk/debian/manifest (rev 0) +++ trunk/packages/spread/trunk/debian/manifest 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,3 @@ +/usr/share/java/spread.jar: + Class-Path: /usr/share/arduino/lib/core.jar /usr/share/java/jebl.jar /usr/share/java/org.boehn.kmlframework.jar /usr/share/java/colt.jar /usr/share/java/ColorPicker.jar + Main-class: gui.SpreadApp Added: trunk/packages/spread/trunk/debian/patches/build_xml.patch =================================================================== --- trunk/packages/spread/trunk/debian/patches/build_xml.patch (rev 0) +++ trunk/packages/spread/trunk/debian/patches/build_xml.patch 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,39 @@ +--- spread-1.0.2.orig/build.xml ++++ spread-1.0.2/build.xml +@@ -34,11 +34,11 @@ + <attribute name="Main-Class" value="${main_class_SpreadApp}" /> + </manifest> + <fileset dir="classes"/> +- <zipgroupfileset dir="lib" includes="core.jar"/> +- <zipgroupfileset dir="lib" includes="jebl.jar"/> +- <zipgroupfileset dir="lib" includes="org.boehn.kmlframework_20090320.jar"/> +- <zipgroupfileset dir="lib" includes="colt.jar"/> +- <zipgroupfileset dir="lib" includes="ColorPicker.jar"/> ++ <zipgroupfileset dir="/usr/share/arduino/lib" includes="core.jar"/> ++ <zipgroupfileset dir="/usr/share/java" includes="jebl.jar"/> ++ <zipgroupfileset dir="/usr/share/java" includes="org.boehn.kmlframework.jar"/> ++ <zipgroupfileset dir="/usr/share/java" includes="colt.jar"/> ++ <zipgroupfileset dir="/usr/share/java" includes="ColorPicker.jar"/> + <!-- + <zipgroupfileset dir="lib" includes="quaqua.jar"/> + --> +--- spread-1.0.2.orig/.classpath ++++ spread-1.0.2/.classpath +@@ -1,12 +1,11 @@ + <?xml version="1.0" encoding="UTF-8"?> + <classpath> + <classpathentry kind="src" path="src"/> +- <classpathentry kind="lib" path="lib/core.jar"/> +- <classpathentry kind="lib" path="lib/jebl.jar"/> +- <classpathentry kind="lib" path="lib/org.boehn.kmlframework_20090320.jar"/> ++ <classpathentry kind="lib" path="/usr/share/arduino/lib/core.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/org.boehn.kmlframework.jar"/> + <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> +- <classpathentry kind="lib" path="lib/colt.jar"/> +- <classpathentry kind="lib" path="lib/ColorPicker.jar"/> +- <classpathentry kind="lib" path="release/Mac/lib/quaqua.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/colt.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/ColorPicker.jar"/> + <classpathentry kind="output" path="bin"/> + </classpath> Added: trunk/packages/spread/trunk/debian/patches/follow_hint_from_README.patch =================================================================== --- trunk/packages/spread/trunk/debian/patches/follow_hint_from_README.patch (rev 0) +++ trunk/packages/spread/trunk/debian/patches/follow_hint_from_README.patch 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,18 @@ +Author: Andreas Tille <[email protected]> +Description: README says: + Before exporting to a runnable jar change line 12 in templates.MapBackground.java: + boolean fromJar = false + to + boolean fromJar = true + +--- spread-1.0.2.orig/src/templates/MapBackground.java ++++ spread-1.0.2/src/templates/MapBackground.java +@@ -11,7 +11,7 @@ + public static int mapImageWidth = 2048; + public static int mapImageHeight = 1025; + +- boolean fromJar = false; ++ boolean fromJar = true; + + public MapBackground(PApplet p) { + Added: trunk/packages/spread/trunk/debian/patches/series =================================================================== --- trunk/packages/spread/trunk/debian/patches/series (rev 0) +++ trunk/packages/spread/trunk/debian/patches/series 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,2 @@ +follow_hint_from_README.patch +build_xml.patch Added: trunk/packages/spread/trunk/debian/rules =================================================================== --- trunk/packages/spread/trunk/debian/rules (rev 0) +++ trunk/packages/spread/trunk/debian/rules 2012-01-26 19:23:44 UTC (rev 9441) @@ -0,0 +1,18 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules file for spread +# Andreas Tille <[email protected]> +# GPL + +#export DH_VERBOSE=1 + +DEBJAR := /usr/share/java +CLASSPATH := $(DEBJAR)/jebl.jar:$(DEBJAR)/colt.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/ColorPicker.jar:/usr/share/arduino/lib/core.jar + +%: + dh $@ --with javahelper + +override_dh_auto_build: + # no idea why setting CLASSPATH explicitely this way, however patching + # build.xml and .classpath seems not to be sufficient + CLASSPATH=$(CLASSPATH) ant jar Property changes on: trunk/packages/spread/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
