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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>
<artifactId>SvAnna</artifactId>
<packaging>pom</packaging>
<modules>
<module>svanna-test</module>
<module>svanna-model</module>
<module>svanna-core</module>
<module>svanna-io</module>
<module>svanna-db</module>
<module>svanna-ingest</module>
<module>svanna-configuration</module>
<module>svanna-cli</module>
<module>svanna-benchmark</module>
</modules>
<groupId>org.monarchinitiative.svanna</groupId>
<version>1.0.4</version>
<name>SvAnna</name>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.0.5</version>
</parent>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<java.version>11</java.version>
<maven.compiler.source>${java.version}</maven.compiler.source>
<maven.compiler.target>${java.version}</maven.compiler.target>
<phenol.version>2.0.0</phenol.version>
<phenopacket-tools.version>1.0.0-RC2</phenopacket-tools.version>
<phenopacket-schema.version>2.0.2</phenopacket-schema.version>
<silent.genes.version>0.2.5</silent.genes.version>
<htsjdk.version>3.0.5</htsjdk.version>
<commons-csv.version>1.7</commons-csv.version>
<commons-io.version>2.8.0</commons-io.version>
<commons-net.version>3.8.0</commons-net.version>
<commons-compress.version>1.24.0</commons-compress.version>
<h2.version>1.4.200</h2.version>
</properties>
<developers>
<developer>
<name>Daniel Danis</name>
<email>daniel.danis@jax.org</email>
<organization>The Jackson Laboratory for Genomic Medicine</organization>
<organizationUrl>https://www.jax.org</organizationUrl>
</developer>
<developer>
<name>Peter N Robinson</name>
<email>peter.robinson@jax.org</email>
<organization>The Jackson Laboratory for Genomic Medicine</organization>
<organizationUrl>https://www.jax.org</organizationUrl>
</developer>
</developers>
<scm>
<connection>scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git</connection>
<developerConnection>scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git</developerConnection>
<url>scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git</url>
<tag>v${project.version}</tag>
</scm>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.monarchinitiative.svart</groupId>
<artifactId>svart</artifactId>
<version>2.0.0-RC1</version>
</dependency>
<dependency>
<groupId>org.monarchinitiative.phenol</groupId>
<artifactId>phenol-core</artifactId>
<version>${phenol.version}</version>
</dependency>
<dependency>
<groupId>org.monarchinitiative.phenol</groupId>
<artifactId>phenol-io</artifactId>
<version>${phenol.version}</version>
</dependency>
<dependency>
<groupId>org.monarchinitiative.phenol</groupId>
<artifactId>phenol-annotations</artifactId>
<version>${phenol.version}</version>
</dependency>
<dependency>
<groupId>org.monarchinitiative.sgenes</groupId>
<artifactId>silent-genes-model</artifactId>
<version>${silent.genes.version}</version>
</dependency>
<dependency>
<groupId>org.monarchinitiative.sgenes</groupId>
<artifactId>silent-genes-gtf</artifactId>
<version>${silent.genes.version}</version>
</dependency>
<dependency>
<groupId>org.monarchinitiative.sgenes</groupId>
<artifactId>silent-genes-jannovar</artifactId>
<version>${silent.genes.version}</version>
</dependency>
<dependency>
<groupId>org.monarchinitiative.sgenes</groupId>
<artifactId>silent-genes-io</artifactId>
<version>${silent.genes.version}</version>
</dependency>
<dependency>
<groupId>org.phenopackets.phenopackettools</groupId>
<artifactId>phenopacket-tools-io</artifactId>
<version>${phenopacket-tools.version}</version>
</dependency>
<dependency>
<groupId>org.phenopackets</groupId>
<artifactId>phenopacket-schema</artifactId>
<version>${phenopacket-schema.version}</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java-util</artifactId>
<version>3.20.1</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>31.1-jre</version>
</dependency>
<dependency>
<groupId>com.google.errorprone</groupId>
<artifactId>error_prone_annotations</artifactId>
<version>2.11.0</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>${htsjdk.version}</version>
<exclusions>
<exclusion>
<groupId>org.tukaani</groupId>
<artifactId>xz</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>${commons-csv.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>${commons-compress.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>commons-net</groupId>
<artifactId>commons-net</artifactId>
<version>${commons-net.version}</version>
</dependency>
<dependency>
<groupId>info.picocli</groupId>
<artifactId>picocli</artifactId>
<version>4.5.2</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.3</version>
</plugin>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<version>2.5.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.3.0</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.8.1</version>
<configuration>
<generateBackupPoms>false</generateBackupPoms>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
</plugin>
</plugins>
</build>
</project>