/
pom.xml
executable file
·393 lines (388 loc) · 13.3 KB
/
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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>Assseq</groupId>
<artifactId>Assseq</artifactId>
<packaging>jar</packaging>
<version>0.4</version>
<name>Assseq</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<project.bundle.mainclass>assseq.Assseq</project.bundle.mainclass>
<project.organization.name>NBIS</project.organization.name>
<project.bundle.appname>Assseq</project.bundle.appname>
<project.bundle.icon>bla</project.bundle.icon>
</properties>
<repositories>
<repository>
<id>ormbunkar-mvn2-repo</id>
<name>ormbunkar-maven-2-repo</name>
<url>http://ormbunkar.se/mvn-repo</url>
</repository>
</repositories>
<build>
<!-- make sure binaries not are filtered - then they will get corrupted-->
<!-- there is one set of files to be filtered and copied and another copied but not filtered-->
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.xml</include>
<include>**/*.properties</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>false</filtering>
<excludes>
<exclude>**/*.xml</exclude>
<exclude>**/*.properties</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.6</version>
<configuration>
<escapeString>\</escapeString>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<source>1.5</source>
<target>1.5</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>unpack-dependencies</id>
<phase>generate-resources</phase>
<goals>
<goal>unpack-dependencies</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<finalName>assseq</finalName>
<appendAssemblyId>false</appendAssemblyId>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>assseq.Assseq</mainClass>
</manifest>
<manifestEntries>
<SplashScreen-Image>img/splash_128x128.png</SplashScreen-Image>
</manifestEntries>
</archive>
</configuration>
<executions>
<execution>
<id>build-jar-to-use-in-win</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<finalName>assseq</finalName>
<fileMode>0755</fileMode>
<outputDirectory>target/windows-version-${project.version}</outputDirectory>
<appendAssemblyId>false</appendAssemblyId>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>assseq.Assseq</mainClass>
</manifest>
<manifestEntries>
<SplashScreen-Image>img/splash_128x128.png</SplashScreen-Image>
</manifestEntries>
</archive>
</configuration>
</execution>
<execution>
<id>build-jar-to-use-for-linux</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<finalName>assseq</finalName>
<fileMode>0755</fileMode>
<outputDirectory>target/linux-version-${project.version}/assseq/</outputDirectory>
<appendAssemblyId>false</appendAssemblyId>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>assseq.Assseq</mainClass>
</manifest>
<manifestEntries>
<SplashScreen-Image>img/splash_128x128.png</SplashScreen-Image>
</manifestEntries>
</archive>
</configuration>
</execution>
<execution>
<id>build-jar-to-use-for-mac</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<finalName>assseq</finalName>
<fileMode>0755</fileMode>
<appendAssemblyId>false</appendAssemblyId>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>assseq.Assseq</mainClass>
</manifest>
<manifestEntries>
<SplashScreen-Image>img/splash_128x128.png</SplashScreen-Image>
</manifestEntries>
</archive>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>truezip-maven-plugin</artifactId>
<version>1.1</version>
<executions>
<execution>
<id>remove-a-file-in-windows-version</id>
<goals>
<goal>remove</goal>
</goals>
<phase>package</phase>
<configuration>
<filesets>
<fileset>
<directory>target/windows-version-${project.version}/assseq.jar</directory>
<includes>
<include>cap3*linux*</include>
<include>cap3*mac*</include>
</includes>
</fileset>
</filesets>
</configuration>
</execution>
<execution>
<id>remove-a-file-in-sub-archive-mac</id>
<goals>
<goal>remove</goal>
</goals>
<phase>package</phase>
<configuration>
<filesets>
<fileset>
<directory>target/assseq.jar</directory>
<includes>
<include>cap3*linux*</include>
<include>cap3*.exe</include>
<include>cygwin*.dll</include>
</includes>
</fileset>
</filesets>
</configuration>
</execution>
<execution>
<id>remove-a-file-in-sub-archive-linux</id>
<goals>
<goal>remove</goal>
</goals>
<phase>package</phase>
<configuration>
<filesets>
<fileset>
<directory>target/linux-version-${project.version}/assseq/assseq.jar</directory>
<includes>
<include>cap3*mac*</include>
<include>cap3*.exe</include>
<include>cygwin*.dll</include>
</includes>
</fileset>
</filesets>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>osxappbundle-maven-plugin</artifactId>
<version>1.0-alpha-2</version>
<configuration>
<mainClass>assseq.Assseq</mainClass>
<dictionaryFile>${basedir}/assseq-mac/Info.plist</dictionaryFile>
<iconFile>${basedir}/src/main/resources/img/alignment_ico.icns</iconFile>
<version>${project.version}</version>
<myClasspath>$JAVAROOT/repo/Assseq/Assseq/${project.version}/Assseq-${project.version}.jar</myClasspath>
<javaApplicationStub>${basedir}/assseq-mac/universalJavaApplicationStub/universalJavaApplicationStub</javaApplicationStub>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>bundle</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>truezip-maven-plugin</artifactId>
<version>1.2</version>
<executions>
<execution>
<id>add-splash-image-mac-version</id>
<goals>
<goal>copy</goal>
</goals>
<phase>package</phase>
<configuration>
<files>
<file>
<source>${basedir}/src/main/resources/img/splash_128x128.png</source>
<outputDirectory>target/Assseq-${project.version}/Assseq.app/Contents/Resources/</outputDirectory>
</file>
</files>
</configuration>
</execution>
<execution>
<id>remove-jar-files-from-osx-bundle-since-they-are-unpacked-in-ailiview-jar-already</id>
<goals>
<goal>remove</goal>
</goals>
<!-- This has to be install phase - because it is not created untill package phase -->
<phase>install</phase>
<configuration>
<filesets>
<fileset>
<directory>${project.build.directory}/${project.build.finalName}-app.zip</directory>
<includes>
<include>**/jebl2</include>
<include>**/commons-lang</include>
<include>**/commons-io</include>
<include>**/log4j</include>
</includes>
</fileset>
</filesets>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.akathist.maven.plugins.launch4j</groupId>
<artifactId>launch4j-maven-plugin</artifactId>
<version>1.7.21</version>
<executions>
<!-- GUI exe -->
<execution>
<id>l4j-gui</id>
<phase>package</phase>
<goals>
<goal>launch4j</goal>
</goals>
<configuration>
<headerType>gui</headerType>
<outfile>target/windows-version-${project.version}/Assseq.exe</outfile>
<jar>target/windows-version-${project.version}/assseq.jar</jar>
<errTitle>App Err</errTitle>
<classPath>
<mainClass>assseq.Assseq</mainClass>
</classPath>
<icon>icon_images/win/alignment_multi.ico</icon>
<jre>
<minVersion>1.5.0</minVersion>
<!--<maxVersion>1.6.0</maxVersion>-->
<initialHeapSize>128</initialHeapSize>
<maxHeapSize>1024</maxHeapSize>
</jre>
<splash>
<file>icon_images/alignment_ico_128x128_transp.bmp</file>
<waitForWindow>true</waitForWindow>
<timeout>60</timeout>
<timeoutErr>true</timeoutErr>
</splash>
<versionInfo>
<fileVersion>1.0.0.0</fileVersion>
<txtFileVersion>1.0.0.0</txtFileVersion>
<fileDescription>Desc</fileDescription>
<copyright>C</copyright>
<productVersion>1.0.0.0</productVersion>
<txtProductVersion>1.0.0.0</txtProductVersion>
<productName>Assseq</productName>
<internalName>Assseq</internalName>
<originalFilename>App.exe</originalFilename>
</versionInfo>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.13</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>jebl2</groupId>
<artifactId>jebl</artifactId>
<version>0.1</version>
</dependency>
<dependency>
<groupId>com.yuvimasory</groupId>
<artifactId>orange-extensions</artifactId>
<version>1.3.0</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.sun.activation</groupId>
<artifactId>javax.activation</artifactId>
<version>1.2.0</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>5.1.1</version>
</dependency>
</dependencies>
</project>