[med-svn] r5913 - trunk/packages/figtree/trunk/debian
Andreas Tille
tille at alioth.debian.org
Sat Feb 5 21:53:47 UTC 2011
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+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 <a.rambaut at ed.ac.uk>
+Source: http://code.google.com/p/figtree/
+
+Files: *
+Copyright: © 2005-2011 Andrew Rambaut <a.rambaut at ed.ac.uk>
+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 <tille at debian.org>
+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 <tille at debian.org>
+# 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 \
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