This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository mauve.
commit b1f76d315c5bce288ed3df5ab99298a2a8fc5ba8 Author: Andreas Tille <[email protected]> Date: Thu Apr 30 13:05:09 2015 +0200 No idea why git import-orig removes debian/ dir if you recreate upstream branch. Simply get debian/ back ... --- 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 + 16 files changed, 610 insertions(+) diff --git a/debian/bin/mauve b/debian/bin/mauve new file mode 100755 index 0000000..f23bdeb --- /dev/null +++ b/debian/bin/mauve @@ -0,0 +1,7 @@ +#! /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 new file mode 100644 index 0000000..e1eea8e --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +mauve (2.4.0+4734-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #??????) + + -- Andreas Tille <[email protected]> Fri, 17 Apr 2015 15:38:22 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..fecfa8f --- /dev/null +++ b/debian/control @@ -0,0 +1,49 @@ +Source: mauve +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 new file mode 100644 index 0000000..516ac9b --- /dev/null +++ b/debian/copyright @@ -0,0 +1,21 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: libMems +Upstream-Contact: Aaron Darling <[email protected]> +Source: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ + +Files: * +Copyright: 2003 - 2014 Aaron Darling -- [email protected] +License: GPL-2+ + +Files: debian/* +Copyright: 2015 Andreas Tille <[email protected]> +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 new file mode 100755 index 0000000..e0b7a45 --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,38 @@ +#!/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}"-"$VERSION" diff --git a/debian/install b/debian/install new file mode 100644 index 0000000..d47d025 --- /dev/null +++ b/debian/install @@ -0,0 +1,3 @@ +debian/bin usr +Mauve.jar usr/share/java +ext usr/share/Mauve \ No newline at end of file diff --git a/debian/mauve.manifest b/debian/mauve.manifest new file mode 100644 index 0000000..1c12b40 --- /dev/null +++ b/debian/mauve.manifest @@ -0,0 +1,2 @@ +usr/share/java/Mauve.jar: + Class-Path: /usr/share/java/biojava.jar /usr/share/java/commons-cli.jar /usr/share/icedtea-web/netx.jar /usr/share/java/zeus-jscl.jar /usr/share/java/dbus.jar /usr/share/java/unix.jar /usr/share/Mauve/ext/goose.jar diff --git a/debian/patches/build_xml.patch b/debian/patches/build_xml.patch new file mode 100644 index 0000000..c3c83b8 --- /dev/null +++ b/debian/patches/build_xml.patch @@ -0,0 +1,284 @@ +Author: Andreas Tille <[email protected]> +Last-Updated: Fri, 17 Apr 2015 15:38:22 +0200 +Description: Drop OSX specific things from build.xml, + Prevent build from calling home at build time + +--- a/build.xml ++++ b/build.xml +@@ -19,7 +19,6 @@ + --> + <!-- deployment locations for standalone releases --> + <property name="deploy.address" value="[email protected]" /> +- <property name="deploy.bareaddress" value="darlinglab.org" /> + <property name="deploy.username" value="darlini8" /> + <property name="deploy.win32.keyfile" value="C:\Documents and Settings\koadman\plonk.ppk" /> + <property name="deploy.serverdir" value="/home3/darlini8/www/mauve/downloads" /> +@@ -44,14 +43,6 @@ + <!-- get any environment variables --> + <property environment="env" /> + +- <!-- osxant.jar creates Mac OS X disk images --> +- <taskdef name="dmg" classname="com.amberarcher.ant.osx.DmgTask"> +- <classpath> +- <pathelement path="${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}:${deploy.serverdir}" /> +- </exec> +- </target> +- ++ + <!-- assumes that passwordless ssh authentication has been configured to the web server --> + <target name="deployLinux" depends="dist"> + <exec executable="scp"> diff --git a/debian/patches/debian_classes.patch b/debian/patches/debian_classes.patch new file mode 100644 index 0000000..46153cd --- /dev/null +++ b/debian/patches/debian_classes.patch @@ -0,0 +1,77 @@ +Author: Andreas Tille <[email protected]> +Last-Updated: Fri, 17 Apr 2015 15:38:22 +0200 +Description: Use Debian packaged classes + +--- a/build.xml ++++ b/build.xml +@@ -30,7 +30,8 @@ + <property name="build" location="bin"/> + <property name="dist" location="dist"/> + <property name="ext" location="ext"/> +- <property name="support" location="build_support"/> ++ <property name="deblib" location="/usr/share/java" /> ++ <property name="support" location="/usr/share/java"/> + + <!-- Make datestamp for update checks --> + <tstamp> +@@ -45,7 +46,7 @@ + + <taskdef resource="net/sf/antcontrib/antcontrib.properties"> + <classpath> +- <pathelement path="${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 new file mode 100644 index 0000000..3eef136 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,3 @@ +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 new file mode 100644 index 0000000..b0151eb --- /dev/null +++ b/debian/patches/use_JConsole_of_zeus-jscl_properly.patch @@ -0,0 +1,68 @@ +From: Markus Koschany <[email protected]> +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 new file mode 100755 index 0000000..68fadd2 --- /dev/null +++ b/debian/rules @@ -0,0 +1,38 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules file for mauve +# Andreas Tille <[email protected]> +# 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 new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..b38c69e --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +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 new file mode 100644 index 0000000..cf22602 --- /dev/null +++ b/debian/watch @@ -0,0 +1 @@ +# There is no tarball download location, libMuscle is only available in SVN -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mauve.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
