/
pom.xml
1168 lines (1168 loc) · 47.3 KB
/
pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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>uk.ac.sanger</groupId>
<artifactId>artemis</artifactId>
<version>18.2.0</version>
<name>Artemis</name>
<description>Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.</description>
<inceptionYear>1998</inceptionYear>
<!-- GitHub repo connection -->
<scm>
<connection>scm:https://github.com/sanger-pathogens/Artemis.git</connection>
<url>https://github.com/sanger-pathogens/Artemis</url>
<developerConnection>scm:https://github.com/sanger-pathogens/Artemis.git</developerConnection>
<tag>HEAD</tag>
</scm>
<organization>
<name>Wellcome Sanger Institute</name>
<url>http://www.sanger.ac.uk/</url>
</organization>
<url>http://sanger-pathogens.github.io/Artemis/</url>
<developers>
<developer>
<name>Kevin Pepper</name>
<email>artemis-help@sanger.ac.uk</email>
<url>http://www.sanger.ac.uk/science/tools/artemis</url>
<organization>Wellcome Sanger Institute</organization>
<organizationUrl>http://www.sanger.ac.uk/</organizationUrl>
<roles>
<role>developer</role>
</roles>
<timezone>GB/London</timezone>
</developer>
</developers>
<licenses>
<license>
<name>The GNU General Public License, Version 3, June 2007</name>
<url>https://raw.githubusercontent.com/sanger-pathogens/Artemis/master/LICENSE</url>
</license>
</licenses>
<issueManagement>
<system>Github</system>
<url>https://github.com/sanger-pathogens/Artemis/issues</url>
</issueManagement>
<mailingLists>
<mailingList>
<name>Artemis support email address</name>
<post>artemis-help@sanger.ac.uk</post>
</mailingList>
</mailingLists>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<ignore.test.failures>true</ignore.test.failures>
<version.file>${project.basedir}/etc/versions</version.file>
<copyright.text>2022 Wellcome Sanger Institute</copyright.text>
<!-- Properties passed into Maven on command line -->
<emboss.installation.root>${env.EMBOSS_ROOT}</emboss.installation.root>
<!-- Application names -->
<artemis.application.name>Artemis</artemis.application.name>
<artemis.chado.application.name>${artemis.application.name} (CHADO)</artemis.chado.application.name>
<act.application.name>ACT</act.application.name>
<act.chado.application.name>${act.application.name} (CHADO)</act.chado.application.name>
<dnaplotter.application.name>Circular-Plot</dnaplotter.application.name>
<bamview.application.name>BamView</bamview.application.name>
<!-- Deployable jar names -->
<artemis.jar.name>artemis.jar</artemis.jar.name>
<act.jar.name>act.jar</act.jar.name>
<bamview.jar.name>bamview.jar</bamview.jar.name>
<dnaplotter.jar.name>dnaplotter.jar</dnaplotter.jar.name>
<!-- Main classes -->
<artemis.main.class>uk.ac.sanger.artemis.components.ArtemisMain</artemis.main.class>
<act.main.class>uk.ac.sanger.artemis.components.ActMain</act.main.class>
<bamview.main.class>uk.ac.sanger.artemis.components.alignment.BamView</bamview.main.class>
<dnaplotter.main.class>uk.ac.sanger.artemis.circular.DNADraw</dnaplotter.main.class>
<!-- Java version-->
<java.compatibility.major.version>9</java.compatibility.major.version>
<osx.bundler.jar>${project.basedir}/maven-lib/appbundler-1.0ea.jar</osx.bundler.jar>
<osx.bundler.volume>Artemis_Tools</osx.bundler.volume>
<osx.bundler.chado.volume>Artemis_Tools_Chado</osx.bundler.chado.volume>
<!-- Assembly folders -->
<windows.assembly.folder>artemis</windows.assembly.folder>
<unix.assembly.folder>artemis</unix.assembly.folder>
<osx.assembly.folder>artemis</osx.assembly.folder>
<!-- Release deliverable folder -->
<release.artifact.folder>${project.build.directory}/release-artifacts</release.artifact.folder>
<windows.release.folder>${release.artifact.folder}/windows-release</windows.release.folder>
<osx.app.folder>${release.artifact.folder}/mac-osx-release</osx.app.folder>
<osx.app.chado.folder>${release.artifact.folder}/mac-osx-chado-release</osx.app.chado.folder>
<unix.release.folder>${release.artifact.folder}/unix-release</unix.release.folder>
<!-- Release file names -->
<unix.release.filename>artemis-unix-release-${project.version}</unix.release.filename>
<windows.release.filename>artemis-windows-release-${project.version}</windows.release.filename>
<osx.release.filename>artemis-macosx-release-${project.version}</osx.release.filename>
<osx.chado.release.filename>artemis-macosx-chado-release-${project.version}</osx.chado.release.filename>
<!-- Mac OS application JVM options -->
<postgres.command.line.arg>-Djdbc.drivers=org.postgresql.Driver</postgres.command.line.arg>
<maxheap.command.line.arg>-mx2g</maxheap.command.line.arg>
<initialheap.command.line.arg>-ms128m</initialheap.command.line.arg>
<noverify.command.line.arg>-noverify</noverify.command.line.arg>
<unixenv.command.line.arg>-Dartemis.environment=UNIX</unixenv.command.line.arg>
<macosx.menuname.command.line.arg>-Dcom.apple.mrj.application.apple.menu.about.name</macosx.menuname.command.line.arg>
<macosx.dock.command.line.arg>-Xdock:name</macosx.dock.command.line.arg>
<macosx.use.menubar.arg>-Dapple.laf.useScreenMenuBar=true</macosx.use.menubar.arg>
<chado.command.line.arg>-Dchado="localhost:5432/databasename?username"</chado.command.line.arg>
<ibatis.command.line.arg>-Dibatis</ibatis.command.line.arg>
<sangeroptions.command.line.arg>-Dsanger_options=yes</sangeroptions.command.line.arg>
<blackbelt.command.line.arg>-Dblack_belt_mode=false</blackbelt.command.line.arg>
<!-- Surefire unit test plugin parameters -->
<unit.test.timeout.ms>8000</unit.test.timeout.ms>
<surefire.num.forks>1</surefire.num.forks>
<default.tests.surefireArgLine>-Xmx4g ${noverify.command.line.arg} ${postgres.command.line.arg} -DEMBOSS_ROOT=${emboss.installation.root} --illegal-access=warn</default.tests.surefireArgLine>
<surefireArgLine>${default.tests.surefireArgLine} -Dtimeout=${unit.test.timeout.ms} -Duse_separate_classloader=false</surefireArgLine>
<!-- Files to exclude from the build, e.g. Mac resource files. -->
<default.file.excludes>**/log4j*.xml META-INF/* **/.DS_Store **/._*</default.file.excludes>
<!-- Etc files to exclude from the build. -->
<etc.file.excludes>*.seq *.fasta *.embl *.tab *.crunch *.genbank</etc.file.excludes>
<!-- Images -->
<artemis.icons.path>${project.basedir}/icons</artemis.icons.path>
<artemis.images.path>${project.basedir}/images</artemis.images.path>
<!-- Default build flag settings -->
<skip.tests>false</skip.tests>
<jarsigner.skip>true</jarsigner.skip>
<skip.artifact.creation>true</skip.artifact.creation>
<skip.coverage.reporting>true</skip.coverage.reporting>
<skip.javadoc>true</skip.javadoc>
</properties>
<dependencies>
<!-- Start of BATIK Jars -->
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-codec -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-codec</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-dom -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-dom</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-ext -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-ext</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-svggen -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-svggen</artifactId>
<version>1.9.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.xmlgraphics/batik-util -->
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-util</artifactId>
<version>1.9.1</version>
</dependency>
<!-- End of BATIK Jars -->
<!-- Start of IBATIS jars -->
<!-- https://mvnrepository.com/artifact/com.ibatis/ibatis (local legacy jar) -->
<dependency>
<groupId>com.ibatis</groupId>
<artifactId>ibatis</artifactId>
<version>2.3.4.726</version>
</dependency>
<!-- This is now out of date but is used by the ibatis jar-->
<!-- https://mvnrepository.com/artifact/cglib/cglib-nodep -->
<dependency>
<groupId>cglib</groupId>
<artifactId>cglib-nodep</artifactId>
<version>2.2</version>
</dependency>
<!-- End of IBATIS jars (local) -->
<dependency>
<groupId>com.sshtools</groupId>
<artifactId>j2ssh-core</artifactId>
<version>0.2.9</version>
</dependency>
<!-- Latest commons logging from 2014! -->
<!-- https://mvnrepository.com/artifact/commons-logging/commons-logging -->
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.2</version>
</dependency>
<!-- End of J2SSH jars (local) -->
<dependency>
<groupId>org.emboss</groupId>
<artifactId>jemboss</artifactId>
<version>1.0</version>
</dependency>
<!-- Very out of date, but using the latest v3 will not compile atm -->
<!-- https://mvnrepository.com/artifact/commons-lang/commons-lang -->
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-net/commons-net -->
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>3.6</version>
</dependency>
<!-- NOTE: IBatis is no longer supported and very out of date -->
<!-- Using the new postgres driver may cause issues - needs testing -->
<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>42.2.5</version>
</dependency>
<!-- Using latest version gives compilation errors! -->
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>1.6</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-api -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>2.17.2</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-core -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>2.17.2</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-1.2-api -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
<version>2.17.2</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.github.broadinstitute/picard -->
<dependency>
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
<version>2.26.11</version>
</dependency>
<!-- Testing only -->
<!-- https://mvnrepository.com/artifact/junit/junit -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-nop</artifactId>
<version>1.7.25</version>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/org.mockito/mockito-core -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>2.23.0</version>
<scope>test</scope>
</dependency>
<!-- End of testing only -->
</dependencies>
<build>
<plugins>
<!-- =================== Enforce at least Maven 3.1 ======================= -->
<plugin>
<inherited>true</inherited>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.4.1</version>
<executions>
<execution>
<id>enforce-maven-3</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>3.1</version>
</requireMavenVersion>
</rules>
<fail>true</fail>
</configuration>
</execution>
</executions>
</plugin>
<!-- ====================== Read signing related properties ======================= -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.0.0</version>
<executions>
<execution>
<id>load-external-properties</id>
<phase>initialize</phase>
<goals>
<goal>read-project-properties</goal>
</goals>
<configuration>
<!-- Build will not fail if properties file is not found, but signing will fail -->
<quiet>true</quiet>
<files>
<file>maven.properties</file>
</files>
</configuration>
</execution>
</executions>
</plugin>
<!-- ============= Install essential old jars into the local Maven repo ============= -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
<executions>
<execution>
<id>install-biojava-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>org.biojava</groupId>
<artifactId>biojava</artifactId>
<version>1.6</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/biojava.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-jemalign-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>org.emboss</groupId>
<artifactId>jemboss</artifactId>
<version>1.0</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/jemAlign.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-j2ssh-core-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>com.sshtools</groupId>
<artifactId>j2ssh-core</artifactId>
<version>0.2.9</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/j2ssh-core.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
<execution>
<id>install-ibatis-jar</id>
<phase>validate</phase>
<goals>
<goal>install-file</goal>
</goals>
<configuration>
<groupId>com.ibatis</groupId>
<artifactId>ibatis</artifactId>
<version>2.3.4.726</version>
<packaging>jar</packaging>
<file>${project.basedir}/lib/ibatis-2.3.4.726.jar</file>
<generatePom>true</generatePom>
</configuration>
</execution>
</executions>
</plugin>
<!-- ========= Store release version number to the Artemis splash screen version file ======== -->
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.8</version>
<executions>
<execution>
<id>updating-software-version-number</id>
<phase>initialize</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
<echo file="${version.file}">Artemis Release ${project.version}${line.separator}ACT Release ${project.version}${line.separator}DNAPlotter Release ${project.version}${line.separator}BamView ${project.version}</echo>
</target>
</configuration>
</execution>
</executions>
</plugin>
<!-- ============================== Copy resources to build folder ======================== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
<executions>
<!-- Copy etc on to classpath -->
<execution>
<id>copy-property-files</id>
<phase>process-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.outputDirectory}/etc</outputDirectory>
<resources>
<resource>
<directory>${project.basedir}/etc</directory>
</resource>
</resources>
</configuration>
</execution>
<execution>
<id>copy-icons-folder</id>
<phase>process-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/icons</outputDirectory>
<resources>
<resource>
<directory>${artemis.icons.path}</directory>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!-- ===================================== Compile ========================================= -->
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<verbose>false</verbose>
<showWarnings>true</showWarnings>
<!-- We use the release option for Java 9+ -->
<release>${java.compatibility.major.version}</release>
<forceJavacCompilerUse>true</forceJavacCompilerUse>
</configuration>
</plugin>
<!-- ============================== Jar customisation ===================================== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<archive>
<manifest>
<addClasspath>false</addClasspath>
</manifest>
<manifestEntries>
<Permissions>all-permissions</Permissions>
<Codebase>*</Codebase>
</manifestEntries>
</archive>
</configuration>
</plugin>
<!-- ============================ Surefire Unit tests ===================================-->
<!-- Runs unit tests. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
<configuration>
<skipTests>${skip.tests}</skipTests>
<trimStackTrace>true</trimStackTrace>
<forkCount>${surefire.num.forks}</forkCount>
<reuseForks>false</reuseForks>
<testFailureIgnore>${ignore.test.failures}</testFailureIgnore>
<argLine>@{surefireArgLine} -Dlog4j.configurationFile=file:${project.build.testOutputDirectory}/log4j.properties</argLine>
<excludes>
<!-- Exclude manual adhoc tests -->
<exclude>**/RunBlastAtNCBITest.*</exclude>
<exclude>**/TestIbatisDAO.*</exclude>
<exclude>**/TestJdbcDAO.*</exclude>
</excludes>
</configuration>
</plugin>
<!-- =========================== Run Jacoco coverage report ==========================-->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.2</version>
<configuration>
<skip>${skip.coverage.reporting}</skip>
</configuration>
<executions>
<execution>
<id>pre-unit-test</id>
<goals>
<goal>prepare-agent</goal>
</goals>
<configuration>
<output>file</output>
<!-- Sets the path to the file which contains the execution data. -->
<destFile>${project.build.directory}/jacoco-ut.exec</destFile>
<!-- Sets the name of the property containing the settings for JaCoCo runtime agent. -->
<propertyName>surefireArgLine</propertyName>
</configuration>
</execution>
<!--
Ensures that the code coverage report for unit tests is created after
unit tests have been run.
-->
<execution>
<id>post-unit-test</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
<configuration>
<dataFile>${project.build.directory}/jacoco-ut.exec</dataFile>
<outputDirectory>${project.build.directory}/coverage-report</outputDirectory>
<excludes>
<exclude>org/**</exclude>
</excludes>
</configuration>
</execution>
</executions>
</plugin>
<!-- ==== Package the code and dependent jars into one executable jar for each applications ===== -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>package-win-artemis-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/win-jars/${artemis.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${artemis.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-artemis-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${artemis.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${artemis.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-win-act-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/win-jars/${act.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${act.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-act-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${act.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${act.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-win-dnaplotter-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/win-jars/${dnaplotter.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${dnaplotter.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-dnaplotter-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${dnaplotter.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${dnaplotter.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-win-bamview-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/win-jars/${bamview.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${bamview.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>${etc.file.excludes}</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
<execution>
<id>package-default-bamview-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/jars/${bamview.jar.name}</outputFile>
<createDependencyReducedPom>false</createDependencyReducedPom>
<minimizeJar>false</minimizeJar>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${bamview.main.class}</Main-Class>
<Permissions>all-permissions</Permissions>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>org.mozilla:rhino:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>org.python:jython:*</artifact>
<excludes>
<exclude>**</exclude>
</excludes>
</filter>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>${default.file.excludes}</exclude>
<exclude>artemis_sqlmap/**</exclude>
<exclude>etc/**</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
<configuration>
<skipAssembly>${skip.artifact.creation}</skipAssembly>
</configuration>
</plugin>
<!-- ============================= Sign executable jar files ============================ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jarsigner-plugin</artifactId>
<version>1.4</version>
<executions>
<execution>
<id>sign-win-jars</id>
<phase>package</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<skip>${jarsigner.skip}</skip>
<verbose>false</verbose>
<processMainArtifact>false</processMainArtifact>
<processAttachedArtifacts>false</processAttachedArtifacts>
<archiveDirectory>target/win-jars</archiveDirectory>
<keystore>${signer-keystore-path}</keystore>
<storetype>${signer-keystore-type}</storetype>
<alias>${signer-keystore-alias}</alias>
<storepass>${signer-keystore-password}</storepass>
<keypass>${signer-keystore-password}</keypass>
<removeExistingSignatures>true</removeExistingSignatures>
<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
</configuration>
</execution>
<execution>
<id>sign-default-jars</id>
<phase>package</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<skip>${jarsigner.skip}</skip>
<verbose>false</verbose>
<processMainArtifact>false</processMainArtifact>
<processAttachedArtifacts>false</processAttachedArtifacts>
<archiveDirectory>target/jars</archiveDirectory>
<keystore>${signer-keystore-path}</keystore>
<storetype>${signer-keystore-type}</storetype>
<alias>${signer-keystore-alias}</alias>
<storepass>${signer-keystore-password}</storepass>
<keypass>${signer-keystore-password}</keypass>
<removeExistingSignatures>true</removeExistingSignatures>
<tsa>http://timestamp.comodoca.com/rfc3161</tsa>
</configuration>
</execution>
</executions>
</plugin>
<!-- ========================== Create release zips ============================ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>create-unix-release</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<outputDirectory>${unix.release.folder}</outputDirectory>
<descriptors>
<descriptor>src/assembly/unix-release-assembly.xml</descriptor>
</descriptors>
<finalName>${unix.release.filename}</finalName>
</configuration>
</execution>
<execution>
<id>create-windows-release</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<outputDirectory>${windows.release.folder}</outputDirectory>
<descriptors>
<descriptor>src/assembly/windows-release-assembly.xml</descriptor>
</descriptors>
<finalName>${windows.release.filename}</finalName>
</configuration>
</execution>
</executions>
<configuration>
<skipAssembly>${skip.artifact.creation}</skipAssembly>
</configuration>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<!-- We need this next bit to get rid of a warning on the enforcer plugin in Eclipse -->
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<versionRange>[1.3.1,)</versionRange>
<goals>
<goal>enforce</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>