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pom.xml
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pom.xml
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>edu.ucsd.msgf</groupId>
<artifactId>MSGFPlus</artifactId>
<version>1.0.0-SNAPSHOT</version>
<name>MSGF-Plus</name>
<properties>
<skipTests>true</skipTests>
</properties>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<resources>
<resource>
<targetPath>.</targetPath>
<directory>src/main/resources</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
<manifest>
<mainClass>edu.ucsd.msjava.ui.MSGFPlus</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<!-- <finalName>${project.artifactId}-${project.version}-jar-w-reduced-deps</finalName> -->
<finalName>${project.artifactId}</finalName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>edu.ucsd.msjava.ui.MSGFPlus</mainClass>
</transformer>
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
<filter>
<artifact>it.unimi.dsi:fastutil</artifact>
<includes>
<!-- Added a maven shade plugin step with minimize-jar set to true to mzIdentML pom to determine the needed fastutil classes.
Then used Beyond Compare 4 to compare the resulting jar vs. the result of this step until the fastutil classes matched. -->
<!-- booleans -->
<include>it/unimi/dsi/fastutil/booleans/BooleanArrays**</include>
<include>it/unimi/dsi/fastutil/booleans/BooleanComparator**</include>
<!-- chars -->
<include>it/unimi/dsi/fastutil/chars/AbstractCharBidirectionalIterator**</include>
<include>it/unimi/dsi/fastutil/chars/AbstractCharCollection**</include>
<include>it/unimi/dsi/fastutil/chars/AbstractCharIterator**</include>
<include>it/unimi/dsi/fastutil/chars/AbstractCharList**</include>
<include>it/unimi/dsi/fastutil/chars/AbstractCharListIterator**</include>
<include>it/unimi/dsi/fastutil/chars/AbstractCharSet**</include>
<include>it/unimi/dsi/fastutil/chars/CharArrayList**</include>
<include>it/unimi/dsi/fastutil/chars/CharArrays**</include>
<include>it/unimi/dsi/fastutil/chars/CharBidirectionalIterator**</include>
<include>it/unimi/dsi/fastutil/chars/CharCollection**</include>
<include>it/unimi/dsi/fastutil/chars/CharComparator**</include>
<include>it/unimi/dsi/fastutil/chars/CharIterable**</include>
<include>it/unimi/dsi/fastutil/chars/CharIterator**</include>
<include>it/unimi/dsi/fastutil/chars/CharIterators**</include>
<include>it/unimi/dsi/fastutil/chars/CharList**</include>
<include>it/unimi/dsi/fastutil/chars/CharListIterator**</include>
<include>it/unimi/dsi/fastutil/chars/CharOpenHashSet**</include>
<include>it/unimi/dsi/fastutil/chars/CharSet**</include>
<include>it/unimi/dsi/fastutil/chars/CharStack**</include>
<!-- ints -->
<include>it/unimi/dsi/fastutil/ints/IntArrays**</include>
<include>it/unimi/dsi/fastutil/ints/IntComparator**</include>
<!-- objects -->
<include>it/unimi/dsi/fastutil/objects/AbstractObjectBidirectionalIterator**</include>
<include>it/unimi/dsi/fastutil/objects/AbstractObjectCollection**</include>
<include>it/unimi/dsi/fastutil/objects/AbstractObjectIterator**</include>
<include>it/unimi/dsi/fastutil/objects/AbstractObjectList**</include>
<include>it/unimi/dsi/fastutil/objects/AbstractObjectListIterator**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectArrayList**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectArrays**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectBidirectionalIterator**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectCollection**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectIterable**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectIterator**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectIterators**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectList**</include>
<include>it/unimi/dsi/fastutil/objects/ObjectListIterator**</include>
<!-- base-level objects -->
<include>it/unimi/dsi/fastutil/Arrays**</include>
<include>it/unimi/dsi/fastutil/BidirectionalIterator**</include>
<include>it/unimi/dsi/fastutil/Hash**</include>
<include>it/unimi/dsi/fastutil/HashCommon**</include>
<include>it/unimi/dsi/fastutil/Stack**</include>
<include>it/unimi/dsi/fastutil/Swapper**</include>
</includes>
<excludes>
<exclude>it/unimi/dsi/fastutil/chars/AbstractChar2**</exclude>
<exclude>it/unimi/dsi/fastutil/chars/Char2**</exclude>
<exclude>it/unimi/dsi/fastutil/ints/IntComparators**</exclude>
<exclude>it/unimi/dsi/fastutil/objects/ObjectCollections**</exclude>
<exclude>it/unimi/dsi/fastutil/objects/ObjectLists**</exclude>
<exclude>it/unimi/dsi/fastutil/chars/CharCollections**</exclude>
<exclude>it/unimi/dsi/fastutil/chars/CharComparators**</exclude>
<exclude>it/unimi/dsi/fastutil/chars/CharLists**</exclude>
<exclude>it/unimi/dsi/fastutil/chars/CharSets**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>**/.svn/**</exclude>
<!-- <exclude>**/*.java</exclude> -->
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>uk.ac.ebi.jmzidml</groupId>
<artifactId>jmzidentml</artifactId>
<version>1.2.7</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>jmzreader</artifactId>
<version>2.0.1</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.systemsbiology.jrap</groupId>
<artifactId>stax</artifactId>
<version>5.2</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
<type>jar</type>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>2.2.7</version>
</dependency>
<dependency>
<groupId>jaxb</groupId>
<artifactId>activation</artifactId>
<version>1.0.2</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.4</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>nexus-ebi-release-repo</id>
<name>The EBI Maven 2 Nexus release repository</name>
<url>http://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
</repository>
<repository>
<id>internal-repo</id>
<name>The internal repository</name>
<url>file:${project.basedir}/repo</url>
</repository>
</repositories>
<organization>
<name>Center for Computational Mass Spectrometry, University of California, San Diego</name>
<url>http://proteomics.ucsd.edu</url>
</organization>
<description>MSGF+</description>
</project>