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pom.xml
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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!--
~ The Exomiser - A tool to annotate and prioritize genomic variants
~
~ Copyright (c) 2016-2022 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>
<groupId>org.monarchinitiative.exomiser</groupId>
<artifactId>exomiser</artifactId>
<version>13.3.0</version>
<packaging>pom</packaging>
<name>exomiser</name>
<description>A toolkit for filtering variants and prioritising genes by phenotype from whole genome or whole exome VCF files.</description>
<url>https://github.com/exomiser/Exomiser</url>
<inceptionYear>2012</inceptionYear>
<licenses>
<license>
<name>GNU AFFERO GENERAL PUBLIC LICENSE, Version 3 (AGPL-3.0)</name>
<url>http://opensource.org/licenses/AGPL-3.0</url>
</license>
</licenses>
<developers>
<developer>
<name>Jules Jacobsen</name>
<email>[email protected]</email>
<organization>Queen Mary University of London</organization>
<organizationUrl>http://qmul.ac.uk</organizationUrl>
</developer>
<developer>
<name>Damian Smedley</name>
<email>[email protected]</email>
<organization>Queen Mary University of London</organization>
<organizationUrl>http://qmul.ac.uk</organizationUrl>
</developer>
<developer>
<name>Peter Robinson</name>
<email>[email protected]</email>
<organization>The Jackson Laboratory for Genomic Medicine</organization>
<organizationUrl>https://www.jax.org/</organizationUrl>
</developer>
</developers>
<scm>
<connection>scm:git:git://github.com/exomiser/Exomiser.git</connection>
<developerConnection>scm:git:[email protected]:exomiser/Exomiser.git</developerConnection>
<url>https://github.com/exomiser/Exomiser/tree/master</url>
</scm>
<ciManagement>
<system>Circle CI</system>
<url>https://circleci.com/gh/exomiser/Exomiser</url>
</ciManagement>
<modules>
<module>phenix-repository</module>
<module>exomiser-core</module>
<module>exomiser-spring-boot-autoconfigure</module>
<module>exomiser-spring-boot-starter</module>
<module>exomiser-spring-boot-test</module>
<module>exomiser-cli</module>
<module>exomiser-data-genome</module>
<module>exomiser-data-phenotype</module>
<module>exomiser-rest-prioritiser</module>
<module>exomiser-web</module>
</modules>
<properties>
<java.version>11</java.version>
<maven.build.timestamp.format>yyyy-MM-dd HH:mm</maven.build.timestamp.format>
<build.timestamp>${maven.build.timestamp}</build.timestamp>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.organization>The Monarch Initiative</project.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
<sonar.organization>exomiser</sonar.organization>
<sonar.language>java</sonar.language>
<jannovar.version>0.41</jannovar.version>
<svart.version>1.0.2</svart.version>
<htsjdk.version>2.24.1</htsjdk.version>
<guava.version>32.0.0-jre</guava.version>
<protobuf.version>3.25.5</protobuf.version>
<spring-boot.version>2.7.7</spring-boot.version>
<docker.base.image>
gcr.io/distroless/java17-debian11@sha256:d5a7bb2b1bcd09d9b7ba7f7b13df39cbb2ab2ff73a0ab834a5769e59229af2f8
</docker.base.image>
<docker.registry>docker.io</docker.registry>
<docker.repository>exomiser</docker.repository>
<!-- These properties are use for the README.md -->
<genome.data.version>2309</genome.data.version>
<phenotype.data.version>2309</phenotype.data.version>
</properties>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-dependencies</artifactId>
<version>${spring-boot.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.monarchinitiative.svart</groupId>
<artifactId>svart</artifactId>
<version>${svart.version}</version>
</dependency>
<!--DI framework -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jdbc</artifactId>
<type>jar</type>
</dependency>
<!--H2 is a very versatile and highly compatible pure java DB-->
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>2.2.220</version>
</dependency>
<!--https://github.com/brettwooldridge/HikariCP/wiki/FAQ#q-how-to-i-properly-enable-preparedstatement-caching-for-postgresql-->
<!-- <dependency>-->
<!-- <groupId>com.impossibl.pgjdbc-ng</groupId>-->
<!-- <artifactId>pgjdbc-ng</artifactId>-->
<!-- <version>0.4</version>-->
<!-- </dependency>-->
<!--HikariCP is a "zero-overhead" production ready JDBC connection pool.
https://github.com/brettwooldridge/HikariCP -->
<dependency>
<groupId>com.zaxxer</groupId>
<artifactId>HikariCP</artifactId>
</dependency>
<!-- Need to override guava to version 21.0 which contains the Java 8 Collectors support on immutable Collections
used by exomiser-core-->
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.google.protobuf/protobuf-java -->
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
<version>${protobuf.version}</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java-util</artifactId>
<version>${protobuf.version}</version>
</dependency>
<!--JSON + YAML deps-->
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-protobuf</artifactId>
</dependency>
<!--Test dependencies-->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.junit.vintage</groupId>
<artifactId>junit-vintage-engine</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- Required to run Mockito with JUnit Jupiter-->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
<!-- ByteBuddy 1.9.0+ required for compiling on Java 11 -->
<dependency>
<groupId>net.bytebuddy</groupId>
<artifactId>byte-buddy</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>com.google.cloud.tools</groupId>
<artifactId>jib-maven-plugin</artifactId>
<version>3.3.0</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<!-- n.b. the wrapper plugin is completely broken and will only work on Maven 3.7.0+ -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-wrapper-plugin</artifactId>
<version>3.0.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.0.0-M5</version>
<!-- Don't enable parallel tests as these will fail in the autoconfigure module due to MVStore
only being able to be opened once by any given JVM -->
<!-- <configuration>-->
<!-- <forkCount>0</forkCount>-->
<!-- </configuration>-->
</plugin>
<plugin>
<groupId>org.sonarsource.scanner.maven</groupId>
<artifactId>sonar-maven-plugin</artifactId>
<version>3.7.0.1746</version>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<executions>
<execution>
<id>prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<phase>test</phase>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<profiles>
<profile>
<id>coverage</id>
<build>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<executions>
<execution>
<id>prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>report</id>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>