Author: mes
Date: 2010-08-03 11:58:42 -0700 (Tue, 03 Aug 2010)
New Revision: 21138
Added:
cytoscape/trunk/application/src/main/assembly/
cytoscape/trunk/application/src/main/assembly/application.xml
cytoscape/trunk/application/src/main/assembly/distribution.xml
cytoscape/trunk/application/src/main/bin/
cytoscape/trunk/application/src/main/licenses/
cytoscape/trunk/application/src/main/sampleData/
Removed:
cytoscape/trunk/application/src/main/bin/cytoscape
cytoscape/trunk/distribution/src/main/bin/
cytoscape/trunk/distribution/src/main/licenses/
cytoscape/trunk/distribution/src/main/sampleData/
Modified:
cytoscape/trunk/application/pom.xml
Log:
moved assembly creation back into application
Modified: cytoscape/trunk/application/pom.xml
===================================================================
--- cytoscape/trunk/application/pom.xml 2010-08-03 18:02:57 UTC (rev 21137)
+++ cytoscape/trunk/application/pom.xml 2010-08-03 18:58:42 UTC (rev 21138)
@@ -122,9 +122,10 @@
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-5</version>
<configuration>
- <descriptorRefs>
- <descriptorRef>jar-with-dependencies</descriptorRef>
- </descriptorRefs>
+ <descriptors>
+ <descriptor>src/main/assembly/application.xml</descriptor>
+ <descriptor>src/main/assembly/distribution.xml</descriptor>
+ </descriptors>
<archive>
<manifest>
<mainClass>cytoscape.CyMain</mainClass>
@@ -471,6 +472,112 @@
<artifactId>jaxb-impl</artifactId>
<version>1.0</version>
</dependency>
+
+
+ <!-- coreplugins -->
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>advanced-network-merge</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>automatic-layout</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>biomart-client</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>biopax</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>editor</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>equation-functions</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>manual-layout</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>ncbi-client</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>psi-mi</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>psi-mi</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>rfilters</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>sbml-reader</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>table-import</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>attribute-browser</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>cpath</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>cpath2</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+ <dependency>
+ <groupId>cytoscape.coreplugins</groupId>
+ <artifactId>linkout</artifactId>
+ <version>2.8.0-SNAPSHOT</version>
+ <classifier>jar-with-dependencies</classifier>
+ </dependency>
+
</dependencies>
</project>
Added: cytoscape/trunk/application/src/main/assembly/application.xml
===================================================================
--- cytoscape/trunk/application/src/main/assembly/application.xml
(rev 0)
+++ cytoscape/trunk/application/src/main/assembly/application.xml
2010-08-03 18:58:42 UTC (rev 21138)
@@ -0,0 +1,24 @@
+<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0
http://maven.apache.org/xsd/assembly-1.1.0.xsd";>
+ <id>jar-with-dependencies</id>
+ <formats>
+ <format>jar</format>
+ </formats>
+ <includeBaseDirectory>false</includeBaseDirectory>
+ <dependencySets>
+ <dependencySet>
+ <excludes>
+ <exclude>cytoscape.coreplugins:*</exclude>
+ </excludes>
+ <unpack>true</unpack>
+ <scope>runtime</scope>
+ </dependencySet>
+ </dependencySets>
+ <fileSets>
+ <fileSet>
+ <directory>${project.build.outputDirectory}</directory>
+ </fileSet>
+ </fileSets>
+</assembly>
+
Added: cytoscape/trunk/application/src/main/assembly/distribution.xml
===================================================================
--- cytoscape/trunk/application/src/main/assembly/distribution.xml
(rev 0)
+++ cytoscape/trunk/application/src/main/assembly/distribution.xml
2010-08-03 18:58:42 UTC (rev 21138)
@@ -0,0 +1,41 @@
+<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0
http://maven.apache.org/xsd/assembly-1.1.0.xsd";>
+ <id>cytoscape</id>
+ <formats>
+ <format>dir</format>
+ </formats>
+ <fileSets>
+ <fileSet>
+ <directory>${basedir}/src/main/bin</directory>
+ <outputDirectory>/</outputDirectory>
+ <fileMode>0755</fileMode>
+ </fileSet>
+ <fileSet>
+ <directory>${basedir}/src/main/licenses</directory>
+ <outputDirectory>licenses</outputDirectory>
+ <fileMode>0644</fileMode>
+ </fileSet>
+ <fileSet>
+ <directory>${basedir}/src/main/sampleData</directory>
+ <outputDirectory>sampleData</outputDirectory>
+ <fileMode>0644</fileMode>
+ </fileSet>
+ </fileSets>
+ <files>
+ <file>
+
<source>target/${artifactId}-${version}-jar-with-dependencies.jar</source>
+ <destName>cytoscape.jar</destName>
+ <fileMode>0755</fileMode>
+ </file>
+ </files>
+ <dependencySets>
+ <dependencySet>
+ <includes>
+ <include>cytoscape.coreplugins:*:jar:jar-with-dependencies</include>
+ </includes>
+ <outputDirectory>plugins</outputDirectory>
+ <unpack>false</unpack>
+ </dependencySet>
+ </dependencySets>
+</assembly>
Deleted: cytoscape/trunk/application/src/main/bin/cytoscape
===================================================================
--- cytoscape/trunk/distribution/src/main/bin/cytoscape 2010-08-03 00:20:21 UTC
(rev 21123)
+++ cytoscape/trunk/application/src/main/bin/cytoscape 2010-08-03 18:58:42 UTC
(rev 21138)
@@ -1,33 +0,0 @@
-#!/bin/bash
-#
-# run cytoscape from a jar file
-#
-# $Revision$
-# $Date$
-#
-# this is a linux-only version
-#-------------------------------------------------------------------------------
-cytoscapeHomeTester=${CYTOSCAPE_HOME:-undefined}
-
-if [ $cytoscapeHomeTester = undefined ]; then
- echo " --- CYTOSCAPE_HOME is undefined, exiting...";
- exit
- else
- if [ -r $CYTOSCAPE_HOME ]; then
- echo $CYTOSCAPE_HOME is readable
- else
- echo $CYTOSCAPE_HOME is defined, but not readable, exiting...
- exit
- fi
- fi
-
-
-export LD_LIBRARY_PATH=$CYTOSCAPE_HOME/lib
-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib
-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/X11R6/lib
-
-java -Xmx1024MB -Djava.library.path=$CYTOSCAPE_HOME \
- -classpath cytoscape.jar:.:$CLASSPATH \
- cytoscape.CyMain \
- -b $CYTOSCAPE_DATA/annotation/manifest $*
-
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