[med-svn] r10971 - in trunk/packages/biojava3/biojava3-live/trunk: . debian debian/source
Olivier Sallou
osallou at alioth.debian.org
Wed May 23 17:14:46 UTC 2012
Author: osallou
Date: 2012-05-23 17:14:45 +0000 (Wed, 23 May 2012)
New Revision: 10971
Added:
trunk/packages/biojava3/biojava3-live/trunk/debian/
trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian
trunk/packages/biojava3/biojava3-live/trunk/debian/README.source
trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.docs
trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.install
trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
trunk/packages/biojava3/biojava3-live/trunk/debian/changelog
trunk/packages/biojava3/biojava3-live/trunk/debian/compat
trunk/packages/biojava3/biojava3-live/trunk/debian/control
trunk/packages/biojava3/biojava3-live/trunk/debian/copyright
trunk/packages/biojava3/biojava3-live/trunk/debian/docs
trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
trunk/packages/biojava3/biojava3-live/trunk/debian/rules
trunk/packages/biojava3/biojava3-live/trunk/debian/source/
trunk/packages/biojava3/biojava3-live/trunk/debian/source/format
trunk/packages/biojava3/biojava3-live/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (3.0.4-1) to trunk
Property changes on: trunk/packages/biojava3/biojava3-live/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/README.Debian 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,6 @@
+biojava for Debian
+------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/README.source
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/README.source (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/README.source 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,9 @@
+biojava for Debian
+------------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.docs
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.docs (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.docs 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1 @@
+#DOCS#
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.install
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.install (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/biojava-doc.install 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1 @@
+#DOCS#
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/build.xml 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,104 @@
+<?xml version="1.0" ?>
+<project name="BJLIB" default="jar" basedir=".">
+ <!-- Directory structure -->
+ <property name="build.dir" location="../build/BJLIB"/>
+ <property name="test.dir" location="../buildtest/BJLIB"/>
+ <property name="dist.dir" location="../dist"/>
+ <property name="src.dir" location="src/main/java"/>
+ <property name="resources.dir" location="src/main/resources"/>
+ <property name="test.src.dir" location="src/test/java"/>
+ <property name="test.resources.dir" location="src/test/resources"/>
+ <property name="lib.dir" location="/usr/share/java"/>
+ <property name="docs.dir" location="../javadoc"/>
+ <property name="docs.lib.dir" location="../doc/BJLIB"/>
+ <property name="class.dir" location="${build.dir}/classes"/>
+ <property name="test.class.dir" location="${test.dir}/classes"/>
+
+ <property name="project.name" value="biojava"/>
+ <property name="debug" value="true"/>
+ <property name="optimized" value="true"/>
+ <property name="project.version" value="1.8.2"/>
+ <property environment="env"/>
+ <property name="project.jarfile.name" value="BJLIB.jar"/>
+
+ <property name="class.path" value="${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar"/>
+
+ <path id="compile.classpath">
+ <fileset dir="${lib.dir}">
+ <include name="commons-cli.jar"/>
+ <include name="commons-collections.jar"/>
+ <include name="commons-dbcp.jar"/>
+ <include name="commons-pool.jar"/>
+ <include name="junit.jar"/>
+ <include name="guava.jar"/>
+ <include name="jgrapht0.8.jar"/>
+ </fileset>
+ <fileset dir="${dist.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ </path>
+
+
+ <target name="clean">
+ <echo level="info">Cleaning build directories</echo>
+ <delete verbose="true" includeEmptyDirs="true">
+ <fileset dir="${build.dir}" includes="**"/>
+ <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
+ </delete>
+ </target>
+
+ <target name="javadocs">
+ <mkdir dir="${docs.dir}"/>
+ <mkdir dir="${docs.lib.dir}"/>
+ <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*">
+ <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
+ </javadoc>
+ </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>
+ <copy todir="${class.dir}" failonerror="false">
+ <fileset dir="${resources.dir}"/>
+ </copy>
+ </target>
+
+ <target name="compile-test">
+ <mkdir dir="${test.class.dir}"/>
+ <javac srcdir="${test.src.dir}" destdir="${test.class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true">
+ </javac>
+ <copy todir="${test.class.dir}" failonerror="false">
+ <fileset dir="${test.resources.dir}"/>
+ </copy>
+ </target>
+
+ <path id="test.classpath">
+ <path refid="compile.classpath"/>
+ <pathelement location="${test.class.dir}" />
+ </path>
+
+ <target name="test" depends="compile-test">
+ <junit haltonfailure="yes" printsummary="yes">
+ <classpath refid="test.classpath"/>
+ <formatter type="plain" usefile="false" />
+ <batchtest>
+ <fileset dir="${test.class.dir}" includes="**/*Test.class" excludes="**/Abstract*.class" />
+ </batchtest>
+ </junit>
+ </target>
+
+ <target name="jar" depends="compile">
+ <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
+ <manifest>
+ <attribute name="Built-By" value="Debian-Med team"/>
+ <attribute name="Class-Path" value="${class.path}"/>
+ <attribute name="Specification-Title" value="BioJava"/>
+ <attribute name="Specification-Version" value="${project.version}"/>
+ </manifest>
+ </jar>
+ </target>
+
+</project>
+
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/changelog (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/changelog 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,9 @@
+biojava3-live (3.0.4-1) UNRELEASED; urgency=low
+
+ * packaging in progress
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ * Dependency on forester (not packaged) http://code.google.com/p/forester/
+
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/compat
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/compat (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/compat 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1 @@
+8
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/control
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/control (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/control 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,72 @@
+Source: biojava3-live
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
+ libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1),
+ libcommons-cli-java, libguava-java (>= 11.0.1),
+ default-jdk, junit4,javahelper (>=0.25), libjgrapht-java,
+ ant-optional
+Build-Depends: debhelper (>= 9), ant
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava3/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/biojava3/trunk/
+Homepage: http://www.biojava.org
+
+Package: libbiojava3.0-java
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libcommons-pool-java (>= 1.1),
+ libcommons-collections-java (>= 2.1),
+ libcommons-dbcp-java (>= 1.1),
+ libhsqldb-java,
+ libbytecode-java
+Suggests: java-virtual-machine, libjgrapht-java, libbiojava3-java, libbiojava3-java-doc
+Description: Java API to biological data and applications (version 1.7)
+ This package presents the Open Source Java API to biological databases
+ and a series of mostly sequence-based algorithms.
+
+Package: libbiojava3-java
+Architecture: all
+Depends: libbiojava3.0-java, ${misc:Depends}
+Description: Java API to biological data and applications (default version)
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+ .
+ BioJava is provided by a vibrant community which meets annually at
+ the Bioinformatics Open Source Conference (BOSC) that traditionally
+ accompanies the Intelligent Systems in Molecular Biology (ISMB)
+ meeting. Much like BioPerl, the employment of this library is valuable
+ for everybody active in the field because of the many tricks of the
+ trade one learns just by communicating on the mailing list.
+ .
+ This is a wrapper package which should enable smooth upgrades to new
+ versions.
+
+Package: libbiojava3-java-demos
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: libbiojava3-java
+Description: Example programs for BioJava
+ The package comes with a wealth of use cases for BioJava. It is generated
+ together with the API documentation but because of its size of ~3.7MB it
+ was decided to distribute it separately.
+
+Package: libbiojava3-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: konqueror|html-browser
+Suggests: libbiojava3-java-demos, libbiojava3-java
+Description: [Biology] Documentation for BioJava
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data.
+ .
+ This package contains the HTML documentation describing the API of BioJava
+ which was generated automatically by JavaDoc.
+
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/copyright (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/copyright 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,38 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: biojava
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package 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 package 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 program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/docs
===================================================================
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download --no-symlink |
+ grep "Newest version on remote site is .* local version is .*" |
+ head -n 1 |
+ sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+
+cd ../tarballs
+#biojava-3.0.4-all.tar.gz
+UTAR="biojava-${VERSION}-all.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv bj${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
+
+cd $PKG-${VERSION}.orig
+ rm -rf biojava3*/target
+cd ..
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig
+rm -rf ${PKG}-${VERSION}.orig
+
+rm ${UTAR}
+
Property changes on: trunk/packages/biojava3/biojava3-live/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/rules
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/rules (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/rules 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,74 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_configure:
+ dh_auto_configure
+ sed -e 's/BJLIB/biojava3-aa-prop/g' debian/build.xml > biojava3-aa-prop/build.xml
+ sed -e 's/BJLIB/biojava3-core/g' debian/build.xml > biojava3-core/build.xml
+ sed -e 's/BJLIB/biojava-alignment/g' debian/build.xml > biojava3-alignment/build.xml
+ sed -e 's/BJLIB/biojava3-genome/g' debian/build.xml > biojava3-genome/build.xml
+ sed -e 's/BJLIB/biojava3-modfinder/g' debian/build.xml > biojava3-modfinder/build.xml
+ sed -e 's/BJLIB/biojava3-phylo/g' debian/build.xml > biojava3-phylo/build.xml
+ sed -e 's/BJLIB/biojava3-sequencing/g' debian/build.xml > biojava3-sequencing/build.xml
+ sed -e 's/BJLIB/biojava3-protein-disorder/g' debian/build.xml > biojava3-protein-disorder/build.xml
+ sed -e 's/BJLIB/biojava3-structure/g' debian/build.xml > biojava3-structure/build.xml
+ sed -e 's/BJLIB/biojava3-ws/g' debian/build.xml > biojava3-ws/build.xml
+ sed -e 's/BJLIB/biojava3-structure-gui/g' debian/build.xml > biojava3-structure-gui/build.xml
+
+override_dh_auto_build:
+ cd biojava3-core && ant jar
+ cd biojava3-phylo && ant jar
+ cd biojava3-alignment && ant jar
+ cd biojava3-aa-prop && ant jar
+ cd biojava3-genome && ant jar
+ cd biojava3-sequencing && ant jar
+ cd biojava3-modfinder && ant jar
+ cd biojava3-protein-disorder && ant jar
+ cd biojava3-structure && ant jar
+ cd biojava3-structure-gui && ant jar
+ cd biojava3-ws && ant jar
+ # make doc
+ rm -rf biojavadoc
+ mkdir biojavadoc
+ cp -r biojava3-*/* biojavadoc/
+ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
+ cd biojavadoc && ant javadocs
+ rm -rf biojavadoc
+
+override_dh_auto_test:
+ cd biojava3-core && ant test
+ cd biojava3-alignment && ant test
+ cd biojava3-aa-prop && ant test
+ cd biojava3-genome && ant test
+ cd biojava3-phylo && ant test
+ cd biojava3-sequencing && ant test
+ cd biojava3-modfinder && ant test
+ cd biojava3-protein-disorder && ant test
+ cd biojava3-structure && ant test
+ cd biojava3-structure-gui && ant test
+ cd biojava3-ws && ant test
+
+
+
+
+override_dh_clean:
+ dh_clean
+ rm -rf build
+ rm -rf dist
+ rm -rf javadoc
+ rm -rf test
+ rm -f biojava3-*/build.xml
+ rm -rf biojavadoc
+
+
+get-orig-source:
+ debian/get-orig-source
+
Property changes on: trunk/packages/biojava3/biojava3-live/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/source/format
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/source/format (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/source/format 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/biojava3/biojava3-live/trunk/debian/watch
===================================================================
--- trunk/packages/biojava3/biojava3-live/trunk/debian/watch (rev 0)
+++ trunk/packages/biojava3/biojava3-live/trunk/debian/watch 2012-05-23 17:14:45 UTC (rev 10971)
@@ -0,0 +1,4 @@
+version=3
+
+http://biojava.org/wiki/BioJava:Download http://biojava.org/download/bj.*/biojava-(.*)-all\.tar\.gz
+
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