[med-svn] [mauve] 01/07: Imported Upstream version 2.4.0+4734
Andreas Tille
tille at debian.org
Thu Apr 30 11:22:24 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mauve.
commit 9687c28cdfdaad196ef049537cef2d5bd0979d62
Author: Andreas Tille <tille at debian.org>
Date: Thu Apr 30 13:04:50 2015 +0200
Imported Upstream version 2.4.0+4734
---
debian/bin/mauve | 7 -
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 49 ----
debian/copyright | 21 --
debian/get-orig-source | 38 ---
debian/install | 3 -
debian/mauve.manifest | 2 -
debian/patches/build_xml.patch | 284 ---------------------
debian/patches/debian_classes.patch | 77 ------
debian/patches/series | 3 -
.../use_JConsole_of_zeus-jscl_properly.patch | 68 -----
debian/rules | 38 ---
debian/source/format | 1 -
debian/upstream/metadata | 12 -
debian/watch | 1 -
ext/goose.jar | Bin 89124 -> 0 bytes
17 files changed, 610 deletions(-)
diff --git a/debian/bin/mauve b/debian/bin/mauve
deleted file mode 100755
index f23bdeb..0000000
--- a/debian/bin/mauve
+++ /dev/null
@@ -1,7 +0,0 @@
-#! /bin/sh
-set -e
-
-# Include the wrappers utility script
-. /usr/lib/java-wrappers/java-wrappers.sh
-
-run_java -Xms128M -Xmx1G -jar /usr/share/java/Mauve.jar "$@"
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index e1eea8e..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-mauve (2.4.0+4734-1) UNRELEASED; urgency=medium
-
- * Initial release (Closes: #??????)
-
- -- Andreas Tille <tille at debian.org> Fri, 17 Apr 2015 15:38:22 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index fecfa8f..0000000
--- a/debian/control
+++ /dev/null
@@ -1,49 +0,0 @@
-Source: mauve
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9),
- javahelper,
- default-jdk,
- ant,
- ant-contrib,
- junit,
- libbiojava-java,
- libcommons-cli-java,
- libdbus-java,
- libzeus-jscl-java,
- icedtea-netx-common,
- libunixsocket-java
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mauve.git
-Vcs-Git: git://anonscm.debian.org/debian-med/mauve.git
-Homepage: http://darlinglab.org/mauve/
-
-Package: mauve
-Architecture: any
-Depends: ${java:Depends},
- ${misc:Depends}
-Recommends: ${java:Recommends},
- libpostgresql-jdbc-java
-Description: multiple genome alignment
- Mauve is a system for efficiently constructing multiple genome alignments
- in the presence of large-scale evolutionary events such as rearrangement
- and inversion. Multiple genome alignment provides a basis for research
- into comparative genomics and the study of evolutionary dynamics. Aligning
- whole genomes is a fundamentally different problem than aligning short
- sequences.
- .
- Mauve has been developed with the idea that a multiple genome aligner
- should require only modest computational resources. It employs algorithmic
- techniques that scale well in the amount of sequence being aligned. For
- example, a pair of Y. pestis genomes can be aligned in under a minute,
- while a group of 9 divergent Enterobacterial genomes can be aligned in
- a few hours.
- .
- Mauve computes and interactively visualizes genome sequence comparisons.
- Using FastA or GenBank sequence data, Mauve constructs multiple genome
- alignments that identify large-scale rearrangement, gene gain, gene loss,
- indels, and nucleotide substutition.
- .
- Mauve is developed at the University of Wisconsin.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 516ac9b..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,21 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: libMems
-Upstream-Contact: Aaron Darling <darling at cs.wisc.edu>
-Source: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/
-
-Files: *
-Copyright: 2003 - 2014 Aaron Darling -- darling at cs.wisc.edu
-License: GPL-2+
-
-Files: debian/*
-Copyright: 2015 Andreas Tille <tille at debian.org>
-License: GPL-2+
-
-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.
- .
- On Debian systems, the complete text of the licenses can be found in:
- GPL-2 - `/usr/share/common-licenses/GPL-2'
diff --git a/debian/get-orig-source b/debian/get-orig-source
deleted file mode 100755
index e0b7a45..0000000
--- a/debian/get-orig-source
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/sh
-# get source for mauve from SVN because there is no source tarball distribution
-
-set -e
-NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-
-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 \([0-9.]\+\) .*${NAME}.*?\1?"`
- if echo "$VERSION" | grep -q "upstream-version" ; then
- echo "Unable to parse version number"
- exit
- fi
-fi
-
-SVNURI="svn://svn.code.sf.net/p/mauve/code/mauve/trunk"
-revision=`LANG=C svn info ${SVNURI} | grep "^Last Changed Rev:" | sed 's/Last Changed Rev: *//'`
-VERSION=`echo ${VERSION}| sed "s/+[0-9]\+$//"`+${revision}
-
-TARDIR=${NAME}-${VERSION}
-
-mkdir -p ../tarballs
-cd ../tarballs
-# svn export conserves time stamps of the files, checkout does not
-LC_ALL=C svn export ${SVNURI} ${TARDIR} >/dev/null 2>/dev/null
-
-cd ${TARDIR}
-rm -rf osx win32 win64
-rm -rf linux-x64/mauveAligner linux-x86/mauveAligner linux-x64/progressiveMauve linux-x86/progressiveMauve
-for libjava in ant bytecode commons-cli core dbus gui jebl jnlp postgres unix zeus-jscl ; do
- find . -name "*${libjava}*.jar" -delete
-done
-rm -rf build_support
-cd ..
-
-tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.xz "${TARDIR}"
-rm -rf "${NAME}"-"$VERSION"
diff --git a/debian/install b/debian/install
deleted file mode 100644
index d47d025..0000000
--- a/debian/install
+++ /dev/null
@@ -1,3 +0,0 @@
-debian/bin usr
-Mauve.jar usr/share/java
-ext usr/share/Mauve
\ No newline at end of file
diff --git a/debian/mauve.manifest b/debian/mauve.manifest
deleted file mode 100644
index 1c12b40..0000000
--- a/debian/mauve.manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-usr/share/java/Mauve.jar:
- Class-Path: /usr/share/java/biojava.jar /usr/share/java/commons-cli.jar /usr/share/icedtea-web/netx.jar /usr/share/java/zeus-jscl.jar /usr/share/java/dbus.jar /usr/share/java/unix.jar /usr/share/Mauve/ext/goose.jar
diff --git a/debian/patches/build_xml.patch b/debian/patches/build_xml.patch
deleted file mode 100644
index c3c83b8..0000000
--- a/debian/patches/build_xml.patch
+++ /dev/null
@@ -1,284 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Updated: Fri, 17 Apr 2015 15:38:22 +0200
-Description: Drop OSX specific things from build.xml,
- Prevent build from calling home at build time
-
---- a/build.xml
-+++ b/build.xml
-@@ -19,7 +19,6 @@
- -->
- <!-- deployment locations for standalone releases -->
- <property name="deploy.address" value="darlini8 at darlinglab.org" />
-- <property name="deploy.bareaddress" value="darlinglab.org" />
- <property name="deploy.username" value="darlini8" />
- <property name="deploy.win32.keyfile" value="C:\Documents and Settings\koadman\plonk.ppk" />
- <property name="deploy.serverdir" value="/home3/darlini8/www/mauve/downloads" />
-@@ -44,14 +43,6 @@
- <!-- get any environment variables -->
- <property environment="env" />
-
-- <!-- osxant.jar creates Mac OS X disk images -->
-- <taskdef name="dmg" classname="com.amberarcher.ant.osx.DmgTask">
-- <classpath>
-- <pathelement path="${support}/osxant.jar"/>
-- </classpath>
-- </taskdef>
-- <!-- maverick-ant.jar supports secure FTP for deployment -->
-- <taskdef name="ssh" classname="com.sshtools.ant.Ssh" classpath="${support}/maverick-ant.jar"/>
- <taskdef resource="net/sf/antcontrib/antcontrib.properties">
- <classpath>
- <pathelement path="${support}/ant-contrib-1.0b3.jar"/>
-@@ -189,7 +180,7 @@
- <copy todir="C:\htdocs" file="./jws/mauve.jnlp" />
- </target>
-
-- <target name="dist" depends="jar,getChangeLog" description="generate the distribution" >
-+ <target name="dist" depends="jar" description="generate the distribution" >
- <!-- Create the distribution directory -->
- <mkdir dir="${dist}" />
-
-@@ -221,146 +212,6 @@
- </tar>
- </target>
-
-- <taskdef name="bundleapp"
-- classname="com.oracle.appbundler.AppBundlerTask"
-- classpath="build_support/appbundler-1.0.jar" />
--
--<!-- Create a DMG - This only works on MacOSX (requires hdiutil) -->
--<target name="dmg" depends="macdist" description="Create a DMG package for MacOSX (only works on MacOSX)">
--
-- <!-- Set this property value to your application name -->
-- <property name="app.name" value="Mauve-${release.version}"/>
--
-- <!-- Set this property value to a directory where you can
-- mount temporarily your images, for example /tmp -->
-- <property name="mountdir" value="/tmp"/>
--
-- <!-- Delete previously created DMG -->
-- <delete file="${dist}/${app.name}.dmg" quiet="yes" failonerror="false"/>
--
-- <!-- Create a temporary Disk Image -->
-- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
-- <arg value="create"/>
-- <arg value="-srcfolder"/>
-- <arg value="staging"/>
-- <arg value="-volname"/>
-- <arg value="${app.name}"/>
-- <arg value="-ov"/>
-- <arg value="${dist}/${app.name}-tmp.dmg"/>
-- <arg value="-format"/>
-- <arg value="UDRW"/>
-- </exec>
--
-- <!-- Attach the temporary image -->
-- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
-- <arg value="attach"/>
-- <arg value="${dist}/${app.name}-tmp.dmg"/>
-- <arg value="-mountroot"/>
-- <arg value="${mountdir}/"/>
-- </exec>
--
-- <!-- Copy the background, the volume icon and DS_Store files -->
-- <mkdir dir="${mountdir}/${app.name}/.background"/>
-- <copy file="osx/background.png" tofile="${mountdir}/${app.name}/.background/background.png" overwrite="true"/>
-- <copy file="osx/mauve.icns" tofile="${mountdir}/${app.name}/.VolumeIcon.icns" overwrite="true"/>
-- <copy file="osx/DS_Store" tofile="${mountdir}/${app.name}/.DS_Store" overwrite="true"/>
--
--
-- <!-- Indicate that we want a custom icon -->
-- <exec executable="SetFile" os="Mac OS X">
-- <arg value="-a"/>
-- <arg value="C"/>
-- <arg value="${mountdir}/${app.name}"/>
-- </exec>
--
-- <!-- Add a symbolic link to the Applications directory -->
-- <symlink link="${mountdir}/${app.name}" resource="/Applications"/>
--
--
--
-- <!-- Detach the temporary image -->
-- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
-- <arg value="detach"/>
-- <arg value="${mountdir}/${app.name}"/>
-- </exec>
--
-- <!-- Compress it to a new image -->
-- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true">
-- <arg value="convert"/>
-- <arg value="${dist}/${app.name}-tmp.dmg"/>
-- <arg value="-format"/>
-- <arg value="UDZO"/>
-- <arg value="-o"/>
-- <arg value="${dist}/${app.name}.dmg"/>
-- </exec>
--
-- <!-- Delete the temporary image -->
-- <delete file="${dist}/${app.name}-tmp.dmg" quiet="yes" failonerror="false"/>
--</target>
--
--
-- <!-- Create an OS X application and disk image -->
-- <target name="macdist" depends="jar,getChangeLog" description="Generate a Mac OS X disk image" >
-- <!-- Create the distribution directory -->
-- <mkdir dir="${dist}" />
-- <delete dir="${dist}/Mauve.app"/>
--
-- <!-- get the java home -->
-- <exec executable="/usr/libexec/java_home" os="Mac OS X" failonerror="true" outputproperty="osx.java.home"/>
-- <bundleapp outputdirectory="${dist}"
-- name="Mauve"
-- displayname="Mauve ${release.version}"
-- identifier="components.Mauve"
-- icon="osx/mauve.icns"
-- shortversion="${release.version}"
-- copyright="(c) 2003-2015 http://darlinglab.org/mauve"
-- mainclassname="org.gel.mauve.gui.Mauve">
-- <classpath file="Mauve.jar" />
-- <classpath file="ext/*.jar" />
-- <librarypath file="osx/progressiveMauve" />
-- <librarypath file="osx/mauveAligner" />
-- <runtime dir="${osx.java.home}" />
-- <option value="-Dapple.laf.useScreenMenuBar=false"/>
-- <option value="-Xmx500m"/>
-- </bundleapp>
--
-- <!-- Create a staging directory for the Disk Image filesystem -->
-- <mkdir dir="staging"/>
-- <exec executable="ditto" failonerror="true">
-- <arg value="-v"/>
-- <arg value="${dist}/Mauve.app"/>
-- <arg value="staging/Mauve.app"/>
-- </exec>
-- <copy todir="staging">
-- <fileset dir="${basedir}">
-- <include name="ChangeLog.html"/>
-- </fileset>
-- </copy>
--
-- <!-- copy text files to the staging directory, adding .txt
-- to their filename -->
-- <copy todir="staging">
-- <fileset dir="${basedir}">
-- <include name="COPYING"/>
-- </fileset>
-- <mapper type="glob" from="*" to="*.txt"/>
-- </copy>
-- <chmod file="staging/Mauve.app/Contents/MacOS/JavaAppLauncher" perm="755"/>
-- <chmod file="staging/Mauve.app/Contents/MacOS/mauveAligner" perm="755"/>
-- <chmod file="staging/Mauve.app/Contents/MacOS/progressiveMauve" perm="755"/>
--
--<!-- sign the app -->
--<exec executable="/usr/bin/codesign" os="Mac OS X" failonerror="true">
-- <arg value="-s"/>
-- <arg value="Developer ID Application: Aaron Darling"/>
-- <arg value="--deep"/>
-- <arg value="staging/Mauve.app"/>
--</exec>
--<!---->
--
--<!-- <dmg destfile="${dist}/Mauve-${release.version}.dmg" name="Mauve ${release.version}" srcdir="staging" compressed="true"/> -->
-- </target>
--
- <target name="srcdist" depends="init" description="package a source distribution">
- <tar destfile="${dist}/mauve_source_${datestamp}.tar.gz" compression="gzip">
- <!-- Copy support files into the dist directory-->
-@@ -384,27 +235,6 @@
- </tar>
- </target>
-
-- <target name="getChangeLog" >
-- <get src="http://darlinglab.org/mauve/user-guide/versions.html" dest="ChangeLog.html" usetimestamp="true"/>
-- <copy file="ChangeLog.html" tofile="ChangeLog"/>
-- </target>
--
-- <target name="nsicompile" depends="jar,getChangeLog" description="make windows installer" >
--
-- <!-- create output directory -->
-- <mkdir dir="${dist}" />
--
-- <!-- Make timestamp and timestampdash for installer making -->
-- <property environment="env" />
-- <echo message="Program files: ${env.ProgramFiles}"/>
-- <exec executable="C:\Program Files (x86)\NSIS\makensis.exe" dir=".">
-- <arg line="/V2 /NOCD win32\mauve.nsi" />
-- <env key="release_version" value="${release.version}" />
-- <env key="datestamp" value="${datestamp}" />
-- </exec>
-- </target>
--
--
- <target name="run" depends="jar" description="run Mauve">
- <java jar="Mauve.jar" fork="true" />
- </target>
-@@ -439,68 +269,8 @@
- </filterset>
- </copy>
-
-- <!-- copy unmodified files to the server -->
-- <ssh host="${deploy.bareaddress}"
-- username="${deploy.username}"
-- version="2"
-- keyfile="${deploy.win32.keyfile}">
-- <sftp action="put" remotedir="${deploy.asapdir}" verbose="true" newer="true">
-- <fileset dir=".">
-- <include name="Mauve.jar" />
-- <include name="mauveApplet.jar" />
-- </fileset>
-- <fileset dir="./ext">
-- <include name="*.jar"/>
-- </fileset>
-- <fileset dir="./src/images">
-- <include name="mauve_icon.gif" />
-- <include name="mauve_logo.png" />
-- </fileset>
-- <fileset dir="${dist}">
-- <include name="mauve.jnlp"/>
-- </fileset>
-- </sftp>
-- <!-- set the permissions so others in the group can modify them -->
-- <exec cmd="chgrp annotation ${deploy.asapdir}/*"/>
-- <exec cmd="chmod 664 ${deploy.asapdir}/*"/>
-- <!-- jar files should have the execute bit set -->
-- <exec cmd="chmod 775 ${deploy.asapdir}/*.jar"/>
-- </ssh>
-- </target>
--
-- <!-- assumes that an ssh key has been registered with the web server -->
-- <target name="deployWin32" depends="nsicompile">
-- <echo file="${dist}\latest" message="${datestamp}"/>
-- <echo file="${dist}\latest.windows" message="${datestamp}"/>
-- <ssh host="${deploy.bareaddress}"
-- username="${deploy.username}"
-- version="2"
-- keyfile="${deploy.win32.keyfile}">
--
-- <sftp action="put" remotedir="${deploy.serverdir}" verbose="true">
-- <fileset dir="${dist}">
-- <include name="mauve_installer_${release.version}.exe"/>
-- <include name="${dist}\latest"/>
-- <include name="${dist}\latest.windows"/>
-- </fileset>
-- </sftp>
-- <exec cmd="cp ${deploy.serverdir}/mauve_installer_${release.version}.exe ${deploy.serverdir}/mauve_installer_${datestamp}.exe"/>
-- </ssh>
- </target>
--
-- <!-- assumes that passwordless ssh authentication has been configured to the web server -->
-- <target name="deployMacOSX" depends="dmg">
-- <exec executable="scp">
-- <arg value="${dist}/Mauve-${release.version}.dmg" />
-- <arg value="${deploy.address}:${deploy.serverdir}" />
-- </exec>
-- <echo file="${dist}/latest.mac" message="${datestamp}"/>
-- <exec executable="scp">
-- <arg value="${dist}/latest.mac" />
-- <arg value="${deploy.address}:${deploy.serverdir}" />
-- </exec>
-- </target>
--
-+
- <!-- assumes that passwordless ssh authentication has been configured to the web server -->
- <target name="deployLinux" depends="dist">
- <exec executable="scp">
diff --git a/debian/patches/debian_classes.patch b/debian/patches/debian_classes.patch
deleted file mode 100644
index 46153cd..0000000
--- a/debian/patches/debian_classes.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Updated: Fri, 17 Apr 2015 15:38:22 +0200
-Description: Use Debian packaged classes
-
---- a/build.xml
-+++ b/build.xml
-@@ -30,7 +30,8 @@
- <property name="build" location="bin"/>
- <property name="dist" location="dist"/>
- <property name="ext" location="ext"/>
-- <property name="support" location="build_support"/>
-+ <property name="deblib" location="/usr/share/java" />
-+ <property name="support" location="/usr/share/java"/>
-
- <!-- Make datestamp for update checks -->
- <tstamp>
-@@ -45,7 +46,7 @@
-
- <taskdef resource="net/sf/antcontrib/antcontrib.properties">
- <classpath>
-- <pathelement path="${support}/ant-contrib-1.0b3.jar"/>
-+ <pathelement path="${support}/ant-contrib.jar"/>
- </classpath>
- </taskdef>
-
-@@ -77,17 +78,14 @@
- <!-- Build all java source files -->
- <javac
- classpath="
-- ${ext}/core-1.9.2-SNAPSHOT.jar;
-- ${ext}/bytecode-1.9.2-SNAPSHOT.jar;
-- ${ext}/gui-1.9.2-SNAPSHOT.jar;
-- ${ext}/commons-cli-1.2.jar;
-+ ${deblib}/biojava.jar;
-+ ${deblib}/commons-cli.jar;
- ${support}/junit.jar;
-- ${ext}/zeus-jscl.jar;
-+ ${deblib}/zeus-jscl.jar;
- ${ext}/goose.jar;
-- ${ext}/ant-1.7.1.jar;
-- ${ext}/dbus-2.6.jar;
-- ${ext}/jebl-0.4.jar;
-- ${ext}/unix-0.5.jar"
-+ ${deblib}/ant.jar;
-+ ${deblib}/dbus.jar;
-+ ${deblib}/unix.jar"
- srcdir="${src}"
- destdir="${build}"
- target="1.6"
---- a/.classpath
-+++ b/.classpath
-@@ -3,18 +3,14 @@
- <classpathentry kind="src" path="src"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="var" path="JUNIT_HOME/junit.jar" sourcepath="ECLIPSE_HOME/plugins/org.eclipse.jdt.source_3.0.0/src/org.junit_3.8.1/junitsrc.zip"/>
-- <classpathentry kind="lib" path="ext/commons-cli-1.2.jar"/>
-- <classpathentry kind="lib" path="ext/ant-1.7.1.jar"/>
-- <classpathentry kind="lib" path="ext/jebl-0.4.jar" sourcepath="/jebl/src"/>
-+ <classpathentry kind="lib" path="/usr/share/java/commons-cli.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/ant.jar"/>
- <classpathentry kind="src" path="test"/>
-- <classpathentry kind="lib" path="ext/zeus-jscl.jar"/>
-- <classpathentry kind="lib" path="ext/dbus-2.6.jar"/>
-- <classpathentry kind="lib" path="ext/unix-0.5.jar"/>
-- <classpathentry kind="lib" path="ext/jsc.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/zeus-jscl.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/dbus.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/unix.jar"/>
- <classpathentry kind="lib" path="ext/goose.jar"/>
-- <classpathentry kind="lib" path="ext/jnlp.jar"/>
-- <classpathentry kind="lib" path="ext/bytecode-1.9.2-SNAPSHOT.jar"/>
-- <classpathentry kind="lib" path="ext/core-1.9.2-SNAPSHOT.jar"/>
-- <classpathentry kind="lib" path="ext/gui-1.9.2-SNAPSHOT.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/icedtea-web/netx.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/>
- <classpathentry kind="output" path="bin"/>
- </classpath>
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 3eef136..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,3 +0,0 @@
-build_xml.patch
-debian_classes.patch
-use_JConsole_of_zeus-jscl_properly.patch
diff --git a/debian/patches/use_JConsole_of_zeus-jscl_properly.patch b/debian/patches/use_JConsole_of_zeus-jscl_properly.patch
deleted file mode 100644
index b0151eb..0000000
--- a/debian/patches/use_JConsole_of_zeus-jscl_properly.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-From: Markus Koschany <apo at gambaru.de>
-Date: Sun, 26 Apr 2015 15:22:19 +0200
-Subject: Adapt to latest libzeus-jscl-java version
- For a detailed explanation see the debian-java mailing list archive
- https://lists.debian.org/debian-java/2015/04/msg00106.html
-
---- a/src/org/gel/mauve/MyConsole.java
-+++ b/src/org/gel/mauve/MyConsole.java
-@@ -10,18 +10,20 @@ import java.io.PrintStream;
- public class MyConsole {
- private static boolean useSwing = false;
-
-- private static JConsole console;
-+ private static JConsole console = new JConsole();
-
- public static void setUseSwing (boolean b) {
- if (b && !useSwing) {
-- console = JConsole.getConsole ();
- console.setTitle ("Mauve Console");
- console.setSize (400, 400);
- Dimension dim = Toolkit.getDefaultToolkit().getScreenSize();
- console.setLocation(dim.width-400, 0);
-- console.startConsole ();
-+ JConsole.getConsole().startConsole ();
-+ if (!console.isVisible()) {
-+ console.setVisible(true);
-+ }
- } else if (!b && useSwing) {
-- console.stopConsole ();
-+ JConsole.getConsole().stopConsole ();
- console = null;
- }
-
-@@ -30,13 +32,13 @@ public class MyConsole {
-
- public static void showConsole () {
- if (useSwing) {
-- console.showConsole ();
-+ JConsole.getConsole().showConsole ();
- }
- }
-
- public static PrintStream err () {
- if (useSwing) {
-- console.showConsole ();
-+ JConsole.getConsole().showConsole ();
- }
- return System.err;
- }
-@@ -44,4 +46,4 @@ public class MyConsole {
- public static PrintStream out () {
- return System.out;
- }
--}
-\ No newline at end of file
-+}
---- a/src/org/gel/mauve/gui/MauveFrame.java
-+++ b/src/org/gel/mauve/gui/MauveFrame.java
-@@ -497,8 +497,7 @@ public class MauveFrame extends JFrame implements ActionListener, ModelProgressL
- }
- if (source == jMenuHelpConsole || ae.getActionCommand().equals("Console"))
- {
-- JConsole console = JConsole.getConsole();
-- console.showConsole();
-+ JConsole.getConsole().showConsole();
- }
- if (source == jMenuHelpClearCache || ae.getActionCommand().equals("ClearCache"))
- {
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 68fadd2..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-# debian/rules file for mauve
-# Andreas Tille <tille at debian.org>
-# GPL
-
-#export DH_VERBOSE=1
-
-PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-
-JAVA_HOME := /usr/lib/jvm/default-java
-
-DEBJAR := /usr/share/java
-CLASS_PATH := $(DEBJAR)/biojava.jar:$(DEBJAR)/commons-cli.jar:$(DEBJAR)/dbus.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/zeus-jscl.jar
-## :$(DEBJAR)/postgresql-jdbc4.jar
-
-# to run the test suite
-JAVA := $(JAVA_HOME)/bin/java
-ANT_HOME := /usr/share/ant
-ANT_BIN := $(ANT_HOME)/bin/ant
-ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
-
-%:
- dh $@ --with javahelper
-
-override_dh_auto_clean:
- echo "Manual cleaning needed since build.xml has no clean target"
- find . -name "*.class" -delete
- rm -rf bin dist
- rm -rf build.number src/version.properties
- rm -rf Mauve.jar ChangeLog*
-
-override_dh_auto_build:
- # CLASSPATH=$(CLASS_PATH)
- ant dist
-
-get-orig-source:
- . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index b38c69e..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,12 +0,0 @@
-Reference:
- Author: "Mauve: multiple alignment of conserved genomic sequence with rearrangements"
- Title: Aaron C. E. Darling and Bob Mau and Frederick R. Blattner and Nicole T. Perna
- Journal: Genome research
- Year: 2004
- Volume: 14
- Number: 7
- Pages: 1394-1403
- DOI: 10.1101/gr.2289704
- PMID: 15231754
- URL: http://genome.cshlp.org/content/14/7/1394.short
- eprint: http://genome.cshlp.org/content/14/7/1394.full.pdf+html
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index cf22602..0000000
--- a/debian/watch
+++ /dev/null
@@ -1 +0,0 @@
-# There is no tarball download location, libMuscle is only available in SVN
diff --git a/ext/goose.jar b/ext/goose.jar
deleted file mode 100644
index a10b37c..0000000
Binary files a/ext/goose.jar and /dev/null differ
--
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