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sblivensbliven
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Changing maven package for protein-comparison-tool to shade
Rather than copy all the jars individually using the maven assembly plugin, we use the shade plugin to combine them all into a single jar file, then assemble that. Since all our dependencies are lgpl-compatible, this should be OK. This fixes biojava#197. I've also included improvements to the run scripts which let you run them from any directory, not just the current one. Maven handles replacing the jar filename at assembly time. Finally, I changed the name of the assembly. They are now named like 'protein-comparison-tool-4.0.0.jar' rather than including a timestamp.
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6 files changed

+127
-52
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6 files changed

+127
-52
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‎pom.xml‎

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@@ -222,6 +222,11 @@
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-shade-plugin</artifactId>
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<version>2.3</version>
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</plugin>
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<plugin>
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<artifactId>maven-assembly-plugin</artifactId>
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<version>2.4</version>

‎protein-comparison-tool/pom.xml‎

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@@ -74,7 +74,70 @@
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-shade-plugin</artifactId>
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<executions>
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<execution>
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<phase>package</phase>
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<goals>
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<goal>shade</goal>
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</goals>
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<configuration>
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<!-- Minimizing removes jmol and log4j -->
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<minimizeJar>false</minimizeJar>
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<artifactSet>
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<excludes>
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<exclude>junit:junit</exclude>
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</excludes>
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</artifactSet>
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<filters>
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<filter>
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<artifact>net.sourceforge.jmol:jmol</artifact>
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<excludes>
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<exclude>javax/vecmath/**</exclude>
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</excludes>
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</filter>
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<filter>
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<artifact>org.biojava:biojava3-structure</artifact>
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<excludes>
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<exclude>demo/DemoFATCAT*</exclude>
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<exclude>demo/DemoCE*</exclude>
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</excludes>
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</filter>
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<filter>
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<!-- Exclude signature files -->
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<artifact>*:*</artifact>
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<excludes>
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<exclude>META-INF/*.SF</exclude>
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<exclude>META-INF/*.DSA</exclude>
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<exclude>META-INF/*.RSA</exclude>
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</excludes>
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</filter>
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</filters>
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<transformers>
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<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
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<manifestEntries>
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<Specification-Vendor>Open Bioinformatics Foundation</Specification-Vendor>
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<Implementation-Vendor>Open Bioinformatics Foundation</Implementation-Vendor>
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<Specification-Version>${project.version}</Specification-Version>
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<Implementation-Version>${project.version}</Implementation-Version>
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<Specification-Title>${project.name}</Specification-Title>
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<Implementation-Title>${project.name}</Implementation-Title>
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<Main-Class>org.biojava.bio.structure.align.gui.AlignmentGui</Main-Class>
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</manifestEntries>
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</transformer>
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<!-- This bit merges the various META-INF/services files -->
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<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
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</transformers>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<configuration>
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<descriptors>
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<goal>single</goal>
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</goals>
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<configuration>
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<finalName>${project.name}_${timestamp}</finalName>
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<finalName>${project.artifactId}-${project.version}</finalName>
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<appendAssemblyId>false</appendAssemblyId>
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</configuration>
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</execution>
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</executions>
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</plugin>
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</plugins>
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</plugins>
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</build>
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</project>

‎protein-comparison-tool/src/main/assembly/assembly.xml‎

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<format>tar.gz</format>
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</formats>
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<!-- <moduleSets>
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<moduleSet>
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<useAllReactorProjects>true</useAllReactorProjects>
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<includes>
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<include>${groupId}:biojava3-core</include>
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<include>${groupId}:biojava3-alignment</include>
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<include>${groupId}:biojava3-structure</include>
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<include>${groupId}:biojava3-structure-gui</include>
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</includes>
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<binaries>
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<outputDirectory>modules/${artifactId}</outputDirectory>
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<outputDirectory>./modules/</outputDirectory>
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<unpack>false</unpack>
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<includeDependencies>true</includeDependencies>
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<dependencySets>
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<dependencySet>
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<unpack>false</unpack>
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<scope>compile</scope>
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</dependencySet>
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</dependencySets>
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</binaries>
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</moduleSet>
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</moduleSets> -->
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<fileSets>
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<fileSet>
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<directory>${project.basedir}/src/main/assembly/</directory>
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<outputDirectory>.</outputDirectory>
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<includes>
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<include>*.sh</include>
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<include>db.out</include>
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<include>example.lst</include>
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<include>LICENSE</include>
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</includes>
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</fileSet>
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<fileSet>
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<directory>${project.build.directory}</directory>
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<outputDirectory>.</outputDirectory>
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<includes>
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<include>${project.build.finalName}.jar</include>
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</includes>
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</fileSet>
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</fileSets>
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<dependencySets>
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<dependencySet>
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<outputDirectory>jars</outputDirectory>
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<includes>
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<include>${groupId}:biojava3-core</include>
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<include>${groupId}:biojava3-alignment</include>
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<include>${groupId}:biojava3-structure</include>
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<include>${groupId}:biojava3-structure-gui</include>
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<include>net.sourceforge.jmol:jmol</include>
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<include>javaws:javaws</include>
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</includes>
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</dependencySet>
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</dependencySets>
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<!-- Shell scripts must be filtered for the correct jar name -->
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<files>
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<file>
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<source>src/main/assembly/runCE.sh</source>
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<outputDirectory>/</outputDirectory>
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<filtered>true</filtered>
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<fileMode>0755</fileMode>
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</file>
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<file>
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<source>src/main/assembly/runFATCAT.sh</source>
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<outputDirectory>/</outputDirectory>
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<filtered>true</filtered>
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<fileMode>0755</fileMode>
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</file>
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<file>
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<source>src/main/assembly/startFarmJob.sh</source>
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<outputDirectory>/</outputDirectory>
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<filtered>true</filtered>
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<fileMode>0755</fileMode>
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</file>
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</files>
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</assembly>

‎protein-comparison-tool/src/main/assembly/runCE.sh‎

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# bash runCE.sh -pdbFilePath /tmp/ -showDBresult db.out
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### Execute jar ###
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# Get the base directory of the argument.
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# Can resolve single symlinks if readlink is installed
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function scriptdir {
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cd "$(dirname "$1")"
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cd "$(dirname "$(readlink "$1" 2>/dev/null || basename "$1" )")"
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pwd
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}
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DIR="$(scriptdir "$0" )"
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# send the arguments to the java app
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# allows to specify a different config file
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args="$*"
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java -Xmx500M -cp "$PWD/jars/*" org.biojava.bio.structure.align.ce.CeMain $args
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java -Xmx500M -cp "$DIR/${project.build.finalName}.jar" org.biojava.bio.structure.align.ce.CeMain "$@"

‎protein-comparison-tool/src/main/assembly/runFATCAT.sh‎

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# for more examples see runCE.sh
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# jCE works almost exactly the same...
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# send the arguments to the java app
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args="$*"
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java -Xmx500M -cp "$PWD/jars/*" org.biojava.bio.structure.align.fatcat.FatCat $args
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### Execute jar ###
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# Get the base directory of the argument.
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# Can resolve single symlinks if readlink is installed
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function scriptdir {
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cd "$(dirname "$1")"
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cd "$(dirname "$(readlink "$1" 2>/dev/null || basename "$1" )")"
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pwd
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}
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DIR="$(scriptdir "$0" )"
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# send the arguments to the java app
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java -Xmx500M -cp "$DIR/${project.build.finalName}.jar" org.biojava.bio.structure.align.fatcat.FatCat "$@"

‎protein-comparison-tool/src/main/assembly/startFarmJob.sh‎

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else
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which java
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java -version
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java -Xmx1G -cp "$PWD/jars/*" org.biojava.bio.structure.align.FarmJob $args
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java -Xmx1G -cp "./${project.build.finalName}.jar" org.biojava.bio.structure.align.FarmJob $args
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fi
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fi
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exit $?
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exit $?

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