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Commit 2ec6dbdb authored by langella's avatar langella
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CMakeList modified to improve debian package build 

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@315 b8ef2a07-7df7-436f-90b9-41648038564b
parent ab9bf0d2
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xtandempipeline/CMakeLists.txt
+ 23
− 15
View file @ 2ec6dbdb
......@@ -8,6 +8,8 @@ SET (Java_JAR_EXECUTABLE "/usr/lib/jvm/java-6-openjdk/bin/jar")
SET (Java_JAVAC_EXECUTABLE "/usr/lib/jvm/java-6-openjdk/bin/javac")
SET (ANT_EXECUTABLE "/usr/bin/ant")
SET (MASCOT_DAT_FILE_JAR "mascotdatfile-3.3.jar")
FIND_PACKAGE( Java REQUIRED )
......@@ -79,6 +81,7 @@ SET(CPACK_SOURCE_IGNORE_FILES
"XTandem_Pipeline.jar"
"XtandemPipeline.jar"
)
# cmake .
# ant -f build_ubuntu.xml copyInShare
# cpack -G TGZ --config CPackSourceConfig.cmake
# dpkg-buildpackage -rfakeroot
......@@ -133,9 +136,14 @@ if (NOT CMAKE_INSTALL_PREFIX)
SET (CMAKE_INSTALL_PREFIX /usr/local)
endif (NOT CMAKE_INSTALL_PREFIX)
configure_file (${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline.desktop.cmake ${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline.desktop)
configure_file (${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline_online.desktop.cmake ${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline_online.desktop)
configure_file (${xtandempipeline_SOURCE_DIR}/share/xtandempipeline/xtandempipeline.sh.cmake ${xtandempipeline_SOURCE_DIR}/share/xtandempipeline/xtandempipeline.sh)
message ("configure ant file build_ubuntu")
configure_file (${xtandempipeline_SOURCE_DIR}/build_ubuntu.xml.cmake ${xtandempipeline_SOURCE_DIR}/build_ubuntu.xml @ONLY)
configure_file (${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline.desktop.cmake ${CMAKE_BINARY_DIR}/share/applications/xtandempipeline.desktop @ONLY)
configure_file (${xtandempipeline_SOURCE_DIR}/share/applications/xtandempipeline_online.desktop.cmake ${CMAKE_BINARY_DIR}/share/applications/xtandempipeline_online.desktop @ONLY)
configure_file (${xtandempipeline_SOURCE_DIR}/share/xtandempipeline/xtandempipeline.sh.cmake ${CMAKE_BINARY_DIR}/share/xtandempipeline/xtandempipeline.sh @ONLY)
configure_file (${xtandempipeline_SOURCE_DIR}/share/xtandempipeline/xtandempipeline.jnlp.cmake ${CMAKE_BINARY_DIR}/share/xtandempipeline/xtandempipeline.jnlp @ONLY)
SET(work_dir ${xtandempipeline_SOURCE_DIR})
MESSAGE ("ANT workdir : ${work_dir} ")
......@@ -151,19 +159,19 @@ ADD_CUSTOM_TARGET(ant_build ALL
#INSTALL(PROGRAMS src/qtbeads/qtbeads DESTINATION bin)
#INSTALL(DIRECTORY doc/man1 DESTINATION share/man/man1)
#INSTALL(FILES doc/man1/beads.1 DESTINATION share/man/man1)
INSTALL(FILES share/applications/xtandempipeline_online.desktop DESTINATION share/applications)
INSTALL(FILES share/applications/xtandempipeline.desktop DESTINATION share/applications)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/applications/xtandempipeline_online.desktop DESTINATION share/applications)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/applications/xtandempipeline.desktop DESTINATION share/applications)
#INSTALL(FILES share/beads/beads_blue.conf DESTINATION share/beads)
#INSTALL(FILES share/beads/beads_silver.conf DESTINATION share/beads)
#INSTALL(FILES share/beads/beads_silver_small.conf DESTINATION share/beads)
INSTALL(PROGRAMS share/xtandempipeline/xtandempipeline.sh DESTINATION bin)
INSTALL(FILES share/xtandempipeline/xtandempipeline.jnlp DESTINATION share/xtandempipeline)
INSTALL(FILES share/xtandempipeline/XtandemPipeline.jar DESTINATION share/xtandempipeline)
INSTALL(FILES share/xtandempipeline/libproteomicsvg.jar DESTINATION share/xtandempipeline)
INSTALL(FILES share/xtandempipeline/libodsstream.jar DESTINATION share/xtandempipeline)
INSTALL(FILES share/xtandempipeline/mascotdatfile-3.2.10.jar DESTINATION share/xtandempipeline)
INSTALL(FILES share/xtandempipeline/cxf-common-utilities-2.2.4.jar DESTINATION share/xtandempipeline)
INSTALL(FILES share/xtandempipeline/PPClient.jar DESTINATION share/xtandempipeline)
INSTALL(FILES share/xtandempipeline/xtandempipeline_icon.svg DESTINATION share/xtandempipeline)
INSTALL(PROGRAMS ${CMAKE_BINARY_DIR}/share/xtandempipeline/xtandempipeline.sh DESTINATION bin)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/xtandempipeline.jnlp DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/XtandemPipeline.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/libproteomicsvg.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/libodsstream.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/${MASCOT_DAT_FILE_JAR} DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/cxf-common-utilities-2.2.4.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${CMAKE_BINARY_DIR}/share/xtandempipeline/PPClient.jar DESTINATION share/xtandempipeline)
INSTALL(FILES ${xtandempipeline_SOURCE_DIR}/share/xtandempipeline/xtandempipeline_icon.svg DESTINATION share/xtandempipeline)
xtandempipeline/build_ubuntu.xml.cmake 0 → 100644
+ 110
− 0
View file @ 2ec6dbdb
<project name="XtandemPipeline" default="jarWithClasspath" basedir=".">
<description>
MyXtandemParser ant build file
</description>
<!-- set global properties for this build -->
<!---Dusr=/usr/local-->
<property name="usr.dir" location="@CMAKE_INSTALL_PREFIX@" />
<property name="sys.dir" location="/usr/share/java" />
<property name="share.dest" location="@CMAKE_BINARY_DIR@/share" />
<property name="share" location="@xtandempipeline_SOURCE_DIR@/share" />
<property name="resources" location="src/resources" />
<property name="src" location="@xtandempipeline_SOURCE_DIR@/src" />
<property name="build" location="@CMAKE_BINARY_DIR@/build" />
<property name="dist" location="@CMAKE_BINARY_DIR@/dist" />
<property name="jnlp" location="@CMAKE_BINARY_DIR@/jnlp" />
<property name="confDest" location="conf" />
<property name="confDir" location="src/conf/release" />
<property name="docDir" location="doc" />
<target name="reset">
<!-- reset the build and dist directory -->
<delete dir="${build}" />
<delete dir="${dist}" />
<mkdir dir="${build}" />
<mkdir dir="${dist}" />
<mkdir dir="${confDest}" />
<!--
<copy file="lib/libproteomicsvg.jar" tofile="${share}/xtandempipeline/libproteomicsvg.jar" overwrite="true" />
<copy file="lib/libodsstream.jar" tofile="${share}/xtandempipeline/libodsstream.jar" overwrite="true" />
-->
</target>
<target name="init" depends="reset">
<!-- Create the time stamp -->
<tstamp />
</target>
<path id="classpath">
<!--xml-apis-ext.jar xml-apis.jar xercesImpl.jar xalan2.jar swt.jar batik.jar liblog4j1.2-java -->
<fileset dir="${sys.dir}" includes="commons-httpclient.jar commons-codec.jar commons-logging.jar log4j-1.2.jar xml-apis-ext.jar xml-apis.jar xercesImpl.jar xalan2.jar swt.jar batik.jar" />
<fileset dir="${share.dest}/xtandempipeline" includes="libproteomicsvg.jar" />
<fileset dir="${share.dest}/xtandempipeline" includes="libodsstream.jar" />
<fileset dir="${share.dest}/xtandempipeline" includes="PPClient.jar" />
<fileset dir="${share.dest}/xtandempipeline" includes="@MASCOT_DAT_FILE_JAR@" />
<fileset dir="${share.dest}/xtandempipeline" includes="cxf-common-utilities-2.2.4.jar" />
</path>
<target name="compile" depends="init" description="compile the source and put in build directory">
<!-- Compile the java code from ${src} into ${build} -->
<copy file="${share}/xtandempipeline/libproteomicsvg.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
<copy file="${share}/xtandempipeline/libodsstream.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
<copy file="${share}/xtandempipeline/PPClient.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
<copy file="${share}/xtandempipeline/@MASCOT_DAT_FILE_JAR@" todir="${share.dest}/xtandempipeline" overwrite="true" />
<copy file="${share}/xtandempipeline/cxf-common-utilities-2.2.4.jar" todir="${share.dest}/xtandempipeline" overwrite="true" />
<javac srcdir="${src}" destdir="${build}" target="1.6" source="1.6" classpathref="classpath" includeantruntime="false">
<compilerarg line="-encoding utf-8" />
<classpath>
<pathelement location="${build}/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.class" />
</classpath>
</javac>
</target>
<target name="jarWithClasspath" depends="compile" description="generates the jar file for Ubuntu">
<mkdir dir="${build}/conf" />
<copy todir="${build}/conf" overwrite="true">
<fileset dir="${confDir}" includes="*" />
</copy>
<copy todir="${build}/fr" overwrite="true">
<fileset dir="${src}/fr" includes="**" />
</copy>
<mkdir dir="${build}/resources" />
<copy todir="${build}/resources" overwrite="true">
<fileset dir="${resources}" includes="**" />
</copy>
<jar jarfile="${share.dest}/xtandempipeline/XtandemPipeline.jar" basedir="${build}">
<!--<fileset dir="${confDir}" />-->
<!--<fileset file=".classpath" />-->
<manifest>
<attribute name="Main-Class" value="fr.inra.pappso.xtandempipeline.XtandemPipelineMain" />
<attribute name="Class-Path" value="${sys.dir}/commons-httpclient.jar ${sys.dir}/commons-codec.jar ${sys.dir}/commons-logging.jar ${sys.dir}/log4j-1.2.jar ${sys.dir}/xml-apis-ext.jar ${sys.dir}/xml-apis.jar ${sys.dir}/xercesImpl.jar ${sys.dir}/xalan2.jar ${sys.dir}/swt.jar ${sys.dir}/batik.jar ${usr.dir}/share/xtandempipeline/libproteomicsvg.jar ${usr.dir}/share/xtandempipeline/libodsstream.jar ${usr.dir}/share/xtandempipeline/PPClient.jar ${usr.dir}/share/xtandempipeline/@MASCOT_DAT_FILE_JAR@ ${usr.dir}/share/xtandempipeline/cxf-common-utilities-2.2.4.jar" />
</manifest>
</jar>
<!-- cd bin; jar -cf client.jar; -->
<!-- <jar jarfile="client.jar" basedir="bin"/> -->
</target>
<target name="clean" depends="jarWithClasspath">
<delete dir="${jnlp}" />
<delete dir="${build}" />
<delete dir="${dist}" />
</target>
<target name="copyInShare" description="copies jar needed by the ubuntu package into the share directory">
<copy file="@xtandempipeline_SOURCE_DIR@/lib/libproteomicsvg.jar" todir="${share}/xtandempipeline" overwrite="true" />
<copy file="@xtandempipeline_SOURCE_DIR@/lib/libodsstream.jar" todir="${share}/xtandempipeline" overwrite="true" />
<copy file="@xtandempipeline_SOURCE_DIR@/lib/PPClient.jar" todir="${share}/xtandempipeline" overwrite="true" />
<copy file="@xtandempipeline_SOURCE_DIR@/lib/@MASCOT_DAT_FILE_JAR@" todir="${share}/xtandempipeline" overwrite="true" />
<copy file="@xtandempipeline_SOURCE_DIR@/lib/cxf-common-utilities-2.2.4.jar" todir="${share}/xtandempipeline" overwrite="true" />
</target>
</project>
xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp.cmake 0 → 100644
+ 103
− 0
View file @ 2ec6dbdb
<?xml version='1.0' encoding='UTF-8'?>
<jnlp codebase="http://pappso.inra.fr/downloads/xtandem_pipeline/" href="http://pappso.inra.fr/bioinfo/xtandempipeline/xtandempipeline.jnlp">
<information>
<title>X!Tandem Pipeline</title>
<vendor>Benoit Valot</vendor>
<homepage href="http://pappso.inra.fr/bioinfo/xtandempipeline"/>
<description>X!Tandem Pipeline</description>
<description kind="short">Logiciel to analyse, filters, view and export X!Tandem results</description>
<icon href="icon_64.png"/>
<shortcut online="false">
<desktop />
</shortcut>
<offline-allowed />
</information>
<security>
<all-permissions />
</security>
<resources>
<jar href="XtandemPipeline.jar" main="true" download="eager" />
<!--
***************************************
batik
**************************
-->
<jar href="lib/batik/batik-anim-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-codec-1.7.jar" main="false" download="eager"/>
<jar href="lib/batik/batik-ext-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-transcoder-1.7.jar" main="false" download="eager"/>
<jar href="lib/batik/batik-script-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-transcoder-1.7.jar" main="false" download="eager"/>
<jar href="lib/batik/batik-awt-util-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-css-1.7.jar" main="false" download="eager"/>
<jar href="lib/batik/batik-gvt-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-svg-dom-1.7.jar" main="false" download="eager"/>
<jar href="lib/batik/batik-util-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-bridge-1.7.jar" main="false" download="eager"/>
<jar href="lib/batik/batik-dom-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-parser-1.7.jar" main="false" download="eager"/>
<jar href="lib/batik/batik-svggen-1.7.jar" main="false" download="eager" />
<jar href="lib/batik/batik-xml-1.7.jar" main="false" download="eager"/>
<!--
***************************************
others
**************************
-->
<jar href="lib/log4j-1.2.jar" main="false" download="eager" />
<jar href="lib/xalan-2.6.0.jar" main="false" download="eager" />
<jar href="lib/xercesImpl-2.9.1.jar" main="false" download="eager" />
<jar href="lib/xml-apis-1.3.04.jar" main="false" download="eager" />
<jar href="lib/xml-apis-ext-1.3.04.jar" main="false" download="eager" />
<jar href="lib/cxf-common-utilities-2.2.4.jar" main="false" download="eager" />
<jar href="lib/@MASCOT_DAT_FILE_JAR@" main="false" download="eager" />
<jar href="lib/PPClient.jar" main="false" download="lazy" />
<jar href="lib/http/commons-codec-1.2.jar" main="false" download="lazy" />
<jar href="lib/http/commons-httpclient-3.1.jar" main="false" download="lazy" />
<jar href="lib/http/commons-logging-1.0.4.jar" main="false" download="lazy" />
<jar href="lib/libproteomicsvg.jar" main="false" download="eager" />
<jar href="lib/libodsstream.jar" main="false" download="eager" />
</resources>
<resources os="Windows" arch="x86">
<j2se version="1.6+" java-vm-args="-Xincgc -Xmx1000m -Xms256m" />
<jar href="lib/swt/swt-win32-windows-x86.jar" />
</resources>
<resources os="Windows" arch="x86_64">
<j2se version="1.6+" java-vm-args="-Xincgc -Xmx1500m -Xms256m" />
<jar href="lib/swt/swt-win32-windows-x86_64.jar" />
</resources>
<resources os="Linux" arch="x86_64">
<j2se version="1.6+" java-vm-args="-Xincgc -Xmx1900m -Xms256m" />
<jar href="lib/swt/swt-gtk-linux-x86_64.jar" />
</resources>
<resources os="Linux" arch="amd64">
<j2se version="1.6+" java-vm-args="-Xincgc -Xmx1900m -Xms256m" />
<jar href="lib/swt/swt-gtk-linux-x86_64.jar" />
</resources>
<resources os="Linux" arch="x86">
<j2se version="1.6+" java-vm-args="-Xincgc -Xmx1400m -Xms256m" />
<jar href="lib/swt/swt-gtk-linux-x86.jar" />
</resources>
<resources os="Linux">
<j2se version="1.6+" java-vm-args="-Xincgc -Xmx1400m -Xms256m" />
<jar href="lib/swt/swt-gtk-linux-x86.jar" />
</resources>
<resources os="Mac\ OS\ X" arch="i386">
<j2se version="1.6+" java-vm-args="-XstartOnFirstThread -Xincgc -Xmx1000m -Xms256m"/>
<jar href="lib/swt/swt-cocoa-macosx-x86.jar" />
</resources>
<resources os="Mac\ OS\ X" arch="x86_64">
<j2se version="1.6+" java-vm-args="-XstartOnFirstThread -Xincgc -Xmx1900m -Xms256m"/>
<jar href="lib/swt/swt-cocoa-macosx-x86_64.jar" />
</resources>
<application-desc main-class="fr.inra.pappso.xtandempipeline.XtandemPipelineMain" >
</application-desc>
<update check="always" policy="prompt-update"></update>
</jnlp>
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