Author: tille Date: 2011-02-12 17:06:39 +0000 (Sat, 12 Feb 2011) New Revision: 5961
Added: trunk/packages/libjebl2-java/ trunk/packages/libjebl2-java/trunk/ trunk/packages/libjebl2-java/trunk/debian/ trunk/packages/libjebl2-java/trunk/debian/changelog trunk/packages/libjebl2-java/trunk/debian/compat trunk/packages/libjebl2-java/trunk/debian/control trunk/packages/libjebl2-java/trunk/debian/copyright trunk/packages/libjebl2-java/trunk/debian/get-orig-source trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs trunk/packages/libjebl2-java/trunk/debian/patches/ trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch trunk/packages/libjebl2-java/trunk/debian/patches/series trunk/packages/libjebl2-java/trunk/debian/rules trunk/packages/libjebl2-java/trunk/debian/source/ trunk/packages/libjebl2-java/trunk/debian/source/format trunk/packages/libjebl2-java/trunk/debian/watch Log: Inject libjebl2-java Added: trunk/packages/libjebl2-java/trunk/debian/changelog =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/changelog (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/changelog 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,5 @@ +jebl2 (0.0.r6-1) unstable; urgency=low + + * Initial Debian Upload (Closes: #??????) + + -- Andreas Tille <[email protected]> Thu, 10 Feb 2011 10:26:38 +0100 Added: trunk/packages/libjebl2-java/trunk/debian/compat =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/compat (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/compat 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1 @@ +7 Added: trunk/packages/libjebl2-java/trunk/debian/control =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/control (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/control 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,43 @@ +Source: jebl2 +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.1), javahelper (>=0.25) +Build-Depends-Indep: default-jdk, default-jdk-doc, libtrove-java, libtrove-java-doc, ant +Standards-Version: 3.9.1 +Section: java +Homepage: http://code.google.com/p/jebl2/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libjebl2-java/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libjebl2-java/trunk/ + + +Package: libjebl2-java +Architecture: all +Depends: ${java:Depends}, ${misc:Depends} +Recommends: ${java:Recommends} +Description: Java Evolutionary Biology Library + A Java library for evolutionary biology and bioinformatics, including + objects representing biomolecular sequences, multiple sequence + alignments and phylogenetic trees. + . + This is a branch of the original JEBL on + http://sourceforge.net/projects/jebl/ to develop a new API and class + library. + + +Package: libjebl2-java-doc +Section: doc +Architecture: all +Depends: ${java:Depends}, ${misc:Depends} +Recommends: ${java:Recommends} +Description: Java Evolutionary Biology Library (documentation) + A Java library for evolutionary biology and bioinformatics, including + objects representing biomolecular sequences, multiple sequence + alignments and phylogenetic trees. + . + This is a branch of the original JEBL on + http://sourceforge.net/projects/jebl/ to develop a new API and class + library. + . + This package provides the documentation for the library Added: trunk/packages/libjebl2-java/trunk/debian/copyright =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/copyright (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/copyright 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,28 @@ +Format: http://dep.debian.net/deps/dep5/ +Upstream-Name: JEBL +Upstream-Contact: Andrew Rambaut <[email protected]> +Source: http://code.google.com/p/jebl2/source/checkout + +Files: * +Copyright: © 2009-2010 Andrew Rambaut <[email protected]> +Licence: 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 Lesser 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/>. +Comment: + On Debian systems, you can read the full text of the GNU Lesser General Public + License in ‘/usr/share/common-licenses/LGPL-3’. + +Files: debian/* +Copyright: © 2011 Andreas Tille <[email protected]> +License: PD + The packaging work is in the public domain unless stated otherwise. Added: trunk/packages/libjebl2-java/trunk/debian/get-orig-source =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/get-orig-source (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/get-orig-source 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,17 @@ +#!/bin/sh +# get source for jebl-lib from SVN + +NAME=jebl2 + +rm -f ../detail +mkdir -p ../tarballs +cd ../tarballs +# svn export concerves time stamps of the files, checkout does not +REV=`LC_ALL=C svn export http://${NAME}.googlecode.com/svn/trunk/ ${NAME} | tail -n 1 | sed 's/^.*revision \([0-9]\+\)./\1/'` +VERSION=0.0.r${REV} + +find ${NAME} -name .svn -type d -exec rm -rf \{\} \; +rm -f ${NAME}/lib/*.jar + +GZIP="--best --no-name" tar -czf "$NAME"_"$VERSION".orig.tar.gz "${NAME}" +rm -rf "${NAME}" Property changes on: trunk/packages/libjebl2-java/trunk/debian/get-orig-source ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/libjebl2-java-doc.javadoc 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1 @@ +doc /usr/share/doc/libjebl2-java/api Added: trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/libjebl2-java.jlibs 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1 @@ +dist/*.jar Added: trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/patches/do_not_build_jam.patch 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,99 @@ +--- jebl2.orig/build.xml ++++ jebl2/build.xml +@@ -7,7 +7,6 @@ + <!-- set global properties for this build --> + <property name="src" location="src"/> + <property name="build" location="build"/> +- <property name="build-mac-only" location="build-mac-only"/> + + <property name="lib" location="lib"/> + <property name="dist" location="dist"/> +@@ -19,31 +18,9 @@ + <tstamp/> + <!-- Create the build directory structure used by compile --> + <mkdir dir="${build}"/> +- <mkdir dir="${build-mac-only}"/> + <mkdir dir="${dist}"/> + </target> + +- <target name="compile-jam" depends="init"> +- <!-- Compile the java code from ${jamsrc} into ${build} --> +- +- <condition property="isMac"> +- <os family="mac"/> +- </condition> +- <javac source="1.5" srcdir="${src}" target="1.5" destdir="${build}" debug="true"> +- <include name="org/**/*"/> +- <exclude name="org/**/maconly/*" unless = "isMac"/> +- </javac> +- +- <!-- Utils.class was getting included in jebl.jar --> +- <!-- twice and Pack200 was having issues. --> +- <!-- Doesn't seem to be the case for me, the class is missing! RM--> +- <!--<delete file="${build}/org/virion/jam/mac/Utils.class"/>--> +- +- <copy todir="${build}"> +- <fileset dir="${src}" includes="org/**/*.png"/> +- </copy> +- </target> +- + <target name="clean"> + <mkdir dir="${build}"/> + <delete includeEmptyDirs="true"> +@@ -52,38 +29,6 @@ + + </target> + +- <target name="compile-jam-mac-only" depends="init"> +- <!-- Compile the java code from ${jamsrc} into ${build} --> +- <condition property="isMac"> +- <os family="mac"/> +- </condition> +- <javac source="1.5" srcdir="${src}" target="1.5" destdir="${build-mac-only}"> +- <include name="org/**/maconly/*"/> +- </javac> +- </target> +- +- <target name="dist-jam-mac-only" depends="compile-jam-mac-only" description="generate the -mac-only distribution"> +- <!-- Create the distribution directory --> +- <mkdir dir="${dist}"/> +- +- <!-- create the mac-only jar file --> +- <jar jarfile="${lib}/jam-mac-only.jar"> +- <fileset dir="${build-mac-only}" includes="**/mac*/**/*.class,*.properties"/> +- </jar> +- </target> +- +- +- <target name="dist-jam" depends="compile-jam" description="generate the JAM distribution"> +- <!-- Create the distribution directory --> +- <mkdir dir="${dist}"/> +- <delete file="${dist}/jam.jar"/> +- <!-- Put everything in ${build} into the jam.jar file --> +- <jar jarfile="${dist}/jam.jar"> +- <fileset dir="${build}" includes="org/**/*.class,org/**/*.properties,org/**/*.png"/> +- <zipgroupfileset dir="${lib}" includes="jam-mac-only.jar"/> +- </jar> +- </target> +- + <target name="compile-jebl" depends="init"> + <!-- Compile the java code from ${src} into ${build} --> + <javac source="1.5" srcdir="${src}" destdir="${build}" debug="true" target="1.5"> +@@ -105,7 +50,7 @@ + </jar> + </target> + +- <target name="dist" depends="dist-jebl,dist-jam" description="generate the distribution"> ++ <target name="dist" depends="dist-jebl" description="generate the distribution"> + <!-- Create the distribution directory --> + <mkdir dir="${dist}"/> + +@@ -116,7 +61,7 @@ + </jar> + </target> + +- <target name="dist-clean" depends="clean,compile-jebl,compile-jam" description="generate the distribution"> ++ <target name="dist-clean" depends="clean,compile-jebl" description="generate the distribution"> + <!-- For some reason I don't fully understand, running the standard distribute + script doesn't always work if you have done a previous build on a previous version + of the source code. For some reason, it just doesn't compile some files. This Added: trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/patches/javadoc.patch 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,25 @@ +--- /dev/null ++++ jebl2/javadoc.xml +@@ -0,0 +1,22 @@ ++<project name="jebl2" default="javadoc" basedir="."> ++ <property name="src" location="src" /> ++ <property name="doc" location="doc" /> ++ <target name="init"> ++ <!-- Create the doc folder --> ++ <mkdir dir="${doc}" /> ++ </target> ++ <target name="javadoc" depends="init" description="generate the javadocs"> ++ <javadoc ++ destdir="${doc}" ++ author="true" ++ version="true" ++ use="true" ++ windowtitle="JEBL2 lib API" ++ access="public"> ++ <packageset dir="${src}" /> ++ <doctitle><![CDATA[<h1>JEBL2</h1>]]></doctitle> ++ <bottom><![CDATA[<i>http://code.google.com/p/jebl2/</i>]]></bottom> ++ <link href="http://java.sun.com/j2se/1.4.1/docs/api/"/> ++ </javadoc> ++ </target> ++</project> Added: trunk/packages/libjebl2-java/trunk/debian/patches/series =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/patches/series (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/patches/series 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,2 @@ +javadoc.patch +do_not_build_jam.patch Added: trunk/packages/libjebl2-java/trunk/debian/rules =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/rules (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/rules 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,17 @@ +#!/usr/bin/make -f + +JAVA_HOME=/usr/lib/jvm/default-java + +%: + dh $@ --with javahelper + +override_dh_auto_clean: + # build.xml does not provide a clean target + rm -rf dist build doc + +override_dh_auto_build: + dh_auto_build + ant -buildfile javadoc.xml + +get-orig-source: + . debian/get-orig-source Property changes on: trunk/packages/libjebl2-java/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/libjebl2-java/trunk/debian/source/format =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/source/format (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/source/format 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/libjebl2-java/trunk/debian/watch =================================================================== --- trunk/packages/libjebl2-java/trunk/debian/watch (rev 0) +++ trunk/packages/libjebl2-java/trunk/debian/watch 2011-02-12 17:06:39 UTC (rev 5961) @@ -0,0 +1,10 @@ +# Obtaining the source tarball of jebl is a bit tricky because there is no +# explicite link to a downloadable tarball on the web page and the source is +# only in SVN. There is even no versioning scheme and this watch file is just +# checking for a new SVN commit + +version=3 +opts="dversionmangle=s/0.0.r//" \ + http://code.google.com/p/jebl2/source/list \ + detail\?r=([\d]+) \ + debian debian/get-orig-source _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
