forked from exomiser/Exomiser
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pom.xml
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pom.xml
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<!--
~ The Exomiser - A tool to annotate and prioritize genomic variants
~
~ Copyright (c) 2016-2019 Queen Mary University of London.
~ Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
~
~ This program is free software: you can redistribute it and/or modify
~ it under the terms of the GNU Affero General Public License as
~ published by the Free Software Foundation, either version 3 of the
~ License, or (at your option) any later version.
~
~ This program is distributed in the hope that it will be useful,
~ but WITHOUT ANY WARRANTY; without even the implied warranty of
~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
~ GNU Affero General Public License for more details.
~
~ You should have received a copy of the GNU Affero General Public License
~ along with this program. If not, see <http://www.gnu.org/licenses/>.
-->
<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>
<artifactId>exomiser-cli</artifactId>
<packaging>jar</packaging>
<name>exomiser-cli</name>
<description>Exomiser command-line interface</description>
<url>https://github.com/exomiser/Exomiser</url>
<parent>
<groupId>org.monarchinitiative.exomiser</groupId>
<artifactId>exomiser</artifactId>
<version>12.1.0</version>
</parent>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.monarchinitiative.exomiser</groupId>
<artifactId>exomiser-spring-boot-starter</artifactId>
<version>${project.parent.version}</version>
</dependency>
<!--commons-cli used for parsing the command line -->
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.3.1</version>
</dependency>
<!-- Caffiene is a newer Java 8 rewrite of GuavaCache-->
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<!--Use filtering so that maven will replace placeholders with values from the pom e.g. ${project.version} -->
<filtering>true</filtering>
<excludes>
<exclude>application.properties</exclude>
<exclude>distribution/*</exclude>
<exclude>examples/*</exclude>
<exclude>vcf/*</exclude>
</excludes>
</resource>
</resources>
<plugins>
<!-- Make an executable jar and specify the main class and classpath -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<!-- set useUniqueVersions=false in order that the
classpath has the SNAPSHOT instead of the build number prefixed to the dependency -->
<useUniqueVersions>false</useUniqueVersions>
<mainClass>org.monarchinitiative.exomiser.cli.Main</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<!-- Specify the dependencies to copy-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.1</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
<includeScope>runtime</includeScope>
</configuration>
</execution>
</executions>
</plugin>
<!-- Specify the resources which need to be made accessible to the user-->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
<executions>
<execution>
<id>copy-resources</id>
<phase>validate</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/distribution-resources</outputDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>application.properties</include>
</includes>
</resource>
<resource>
<directory>src/main/resources/data</directory>
<includes>
<include>*.ser</include>
<include>*.tsv.gz</include>
<include>*.tsv.gz.tbi</include>
</includes>
</resource>
<resource>
<directory>src/main/resources/examples</directory>
<filtering>true</filtering>
<includes>
<include>*.settings</include>
<include>*.yml</include>
<include>test-analysis-batch.txt</include>
<include>test-batchFiles.txt</include>
</includes>
</resource>
<resource>
<directory>src/main/resources/vcf</directory>
<includes>
<include>Pfeiffer.vcf</include>
<include>Pfeiffer-quartet.vcf.gz</include>
<include>Pfeiffer-quartet.ped</include>
<include>*.vcf</include>
<include>*.vcf.gz</include>
</includes>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!--This plugin assembles the various elements together into a redistributable zip/tar.gz file -->
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<descriptors>
<descriptor>src/assemble/distribution.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>