Author: tille Date: 2011-02-05 21:53:45 +0000 (Sat, 05 Feb 2011) New Revision: 5913
Added: trunk/packages/figtree/trunk/debian/changelog trunk/packages/figtree/trunk/debian/compat trunk/packages/figtree/trunk/debian/control trunk/packages/figtree/trunk/debian/copyright trunk/packages/figtree/trunk/debian/figtree-wrapper trunk/packages/figtree/trunk/debian/figtree.examples trunk/packages/figtree/trunk/debian/figtree.install trunk/packages/figtree/trunk/debian/get-orig-source trunk/packages/figtree/trunk/debian/rules trunk/packages/figtree/trunk/debian/watch Log: Added packaging stuff for figtree Added: trunk/packages/figtree/trunk/debian/changelog =================================================================== --- trunk/packages/figtree/trunk/debian/changelog (rev 0) +++ trunk/packages/figtree/trunk/debian/changelog 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1,5 @@ +figtree (1.3.1-1) unstable; urgency=low + + * Initial release (Closes: #????) + + -- Andreas Tille <[email protected]> Thu, 03 Feb 2011 23:48:18 +0100 Added: trunk/packages/figtree/trunk/debian/compat =================================================================== --- trunk/packages/figtree/trunk/debian/compat (rev 0) +++ trunk/packages/figtree/trunk/debian/compat 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1 @@ +7 Added: trunk/packages/figtree/trunk/debian/control =================================================================== --- trunk/packages/figtree/trunk/debian/control (rev 0) +++ trunk/packages/figtree/trunk/debian/control 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1,19 @@ +Source: figtree +Section: non-free/science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.1), openjdk-6-jdk +Standards-Version: 3.9.1 +Homepage: http://tree.bio.ed.ac.uk/software/figtree/ +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/figtree/trunk +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/figtree/trunk/?rev=0&sc=0 + +Package: figtree +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, openjdk-6-jre | java-jre +Description: graphical phylogenetic tree viewer + FigTree is designed as a graphical viewer of phylogenetic trees and as + a program for producing publication-ready figures. In particular it is + designed to display summarized and annotated trees produced by BEAST. Added: trunk/packages/figtree/trunk/debian/copyright =================================================================== --- trunk/packages/figtree/trunk/debian/copyright (rev 0) +++ trunk/packages/figtree/trunk/debian/copyright 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1,34 @@ +Format: http://dep.debian.net/deps/dep5/ +Upstream-Name: FigTree +Upstream-Contact: Andrew Rambaut <[email protected]> +Source: http://code.google.com/p/figtree/ + +Files: * +Copyright: © 2005-2011 Andrew Rambaut <[email protected]> +License: GPL + 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 2 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 package; if not, write to the Free + Software Foundation, Inc., 51 Franklin St, Fifth Floor, + Boston, MA 02110-1301 USA + . + On Debian systems, the full text of the GNU General Public + License version 2 can be found in the file + `/usr/share/common-licenses/GPL'. + + +Files: debian/* +Copyright: © 2011 Andreas Tille <[email protected]> +License: PD + The packaging work is in the public domain unless stated otherwise. Added: trunk/packages/figtree/trunk/debian/figtree-wrapper =================================================================== --- trunk/packages/figtree/trunk/debian/figtree-wrapper (rev 0) +++ trunk/packages/figtree/trunk/debian/figtree-wrapper 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1,30 @@ +#!/bin/sh +# Simple wrapper script used to start FigTree in Debian +set -e + +# If OpenJDK 6 is only available headless, do not try it +if dpkg --get-selections openjdk-6-jre | grep install$ > /dev/null ; then + JAVA_CMDS="$JAVA_HOME/bin/java /usr/lib/jvm/java-6-openjdk/bin/java /usr/lib/jvm/java-6-sun/bin/java" +else + JAVA_CMDS="$JAVA_HOME/bin/java /usr/lib/jvm/java-6-sun/bin/java" +fi + +for jcmd in $JAVA_CMDS; do + if [ "z$ALTERNATIVE_JDK" = "z`readlink -n -f $jcmd`" ] && [ -z "${JAVACMD}" ]; then + JAVACMD="$jcmd" + fi +done + +for jcmd in $JAVA_CMDS; do + if [ -x "$jcmd" -a -z "${JAVACMD}" ]; then + JAVACMD="$jcmd" + fi +done + +if [ "$JAVACMD" ]; then + echo "Using $JAVACMD to execute FigTree." + exec $JAVACMD $JAVA_OPTS -jar /usr/share/figtree/figtree.jar "$@" +else + echo "No valid JVM found to run FigTree." + exit 1 +fi Property changes on: trunk/packages/figtree/trunk/debian/figtree-wrapper ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/figtree/trunk/debian/figtree.examples =================================================================== --- trunk/packages/figtree/trunk/debian/figtree.examples (rev 0) +++ trunk/packages/figtree/trunk/debian/figtree.examples 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1 @@ +examples Added: trunk/packages/figtree/trunk/debian/figtree.install =================================================================== --- trunk/packages/figtree/trunk/debian/figtree.install (rev 0) +++ trunk/packages/figtree/trunk/debian/figtree.install 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1 @@ +dist/*.jar usr/share/figtree Added: trunk/packages/figtree/trunk/debian/get-orig-source =================================================================== --- trunk/packages/figtree/trunk/debian/get-orig-source (rev 0) +++ trunk/packages/figtree/trunk/debian/get-orig-source 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1,39 @@ +#!/bin/sh +# Obtaining the source tarball of FigTree is a bit tricky because here is no +# explicite link to a downloadable tarball on the web page and the source is +# only in SVN + +PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\) .*download.html.*?\1?'` + +if [ "$VERSION" = "" ] ; then + VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $$2 }'` +fi +if echo "$VERSION" | grep -q "upstream-version" ; then + echo "Unable to parse version number" + exit +fi + +cd .. +rm -f download.html +mkdir -p tarballs +cd tarballs + +svn checkout http://figtree.googlecode.com/svn/trunk/ + +# FIXME: Replace this by mv once the script is sufficiently tested +cp -a trunk ${PKG}-${VERSION} + +# remove .svn dirs taht do not belong into upstream tarball +find ${PKG}-${VERSION} -type d -name .svn -exec rm -rf \{\} \; 2>/dev/null + +# fix some broken permissions +for ext in icns jar java jnilib pdf png psd pdf tif ; do + find ${PKG}-${VERSION} -type f -name "*.${ext}" -exec chmod 644 \{\} \; +done + +# remove unneeded OSes +rm -rf ${PKG}-${VERSION}/release/Mac ${PKG}-${VERSION}/release/Windows + +GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "$PKG"-"$VERSION" +rm -rf "$PKG"-"$VERSION" Property changes on: trunk/packages/figtree/trunk/debian/get-orig-source ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/figtree/trunk/debian/rules =================================================================== --- trunk/packages/figtree/trunk/debian/rules (rev 0) +++ trunk/packages/figtree/trunk/debian/rules 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1,14 @@ +#!/usr/bin/make -f +# debian/rules for figtree +# Andreas Tille <[email protected]> +# GPL + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ + +override_dh_auto_clean: + rm -rf dist + ant clean Property changes on: trunk/packages/figtree/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/figtree/trunk/debian/watch =================================================================== --- trunk/packages/figtree/trunk/debian/watch (rev 0) +++ trunk/packages/figtree/trunk/debian/watch 2011-02-05 21:53:45 UTC (rev 5913) @@ -0,0 +1,10 @@ +# Obtaining the source tarball of FigTree is a bit tricky because here is no +# explicite link to a downloadable tarball on the web page and the source is +# only in SVN + +version=3 +http://tree.bio.ed.ac.uk/software/figtree/ \ + /download\.html\?name=figtree&version=v([\d.]*).id=\d+&num=3 \ + debian debian/get-orig-source + +# /download.html?name=figtree&version=v(.*)&id=82&num=3 \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
