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pom.xml
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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>com.hartwig</groupId>
<artifactId>hmftools</artifactId>
<packaging>pom</packaging>
<version>local-SNAPSHOT</version>
<name>HMF Genomics Tools</name>
<modules>
<module>amber</module>
<module>bam-tools</module>
<module>chord</module>
<module>cider</module>
<module>cobalt</module>
<module>compar</module>
<module>crest</module>
<module>cuppa</module>
<module>esvee</module>
<module>fastq-tools</module>
<module>gene-utils</module>
<module>gripss</module>
<module>health-checker</module>
<module>hmf-common</module>
<module>hmf-id-generator</module>
<module>isofox</module>
<module>lilac</module>
<module>linx</module>
<module>neo</module>
<module>orange</module>
<module>orange-datamodel</module>
<module>paddle</module>
<module>patient-db</module>
<module>purple</module>
<module>pave</module>
<module>peach</module>
<module>redux</module>
<module>sage</module>
<module>sigs</module>
<module>sv-tools</module>
<module>teal</module>
<module>virus-interpreter</module>
<module>v-chord</module>
<module>wisp</module>
</modules>
<properties>
<timestamp>${maven.build.timestamp}</timestamp>
<maven.build.timestamp.format>yyyy-MM-dd HH:mm</maven.build.timestamp.format>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.version>11</java.version>
<maven.compiler.plugin.version>3.8.1</maven.compiler.plugin.version>
<maven.assembly.plugin.version>3.0.0</maven.assembly.plugin.version>
<maven.jar.plugin.version>2.4</maven.jar.plugin.version>
<maven.surefire.plugin.version>2.22.2</maven.surefire.plugin.version>
<maven.site.plugin.version>3.7.1</maven.site.plugin.version>
<maven.exec.plugin.version>1.6.0</maven.exec.plugin.version>
<maven.shade.plugin.version>3.2.4</maven.shade.plugin.version>
<hmf-common.version>local-SNAPSHOT</hmf-common.version>
<amber.version>4.1</amber.version>
<bam-tools.version>1.3</bam-tools.version>
<chord.version>2.1.0</chord.version>
<cuppa.version>2.2.1</cuppa.version>
<cider.version>1.0.2</cider.version>
<cobalt.version>2.0</cobalt.version>
<compar.version>1.3</compar.version>
<crest.version>1.0.0</crest.version>
<cuppa.version>2.3</cuppa.version>
<esvee.version>1.0</esvee.version>
<fastq-tools.version>1.0</fastq-tools.version>
<gene-utils.version>1.2</gene-utils.version>
<gripss.version>2.4</gripss.version>
<health-checker.version>3.6</health-checker.version>
<hmf-id-generator.version>3.1</hmf-id-generator.version>
<isofox.version>1.7.1</isofox.version>
<lilac.version>1.7</lilac.version>
<linx.version>2.0</linx.version>
<neo.version>1.2</neo.version>
<orange.version>3.7.1</orange.version>
<orange-datamodel.version>2.7.0</orange-datamodel.version>
<paddle.version>1.1</paddle.version>
<patient-db.version>6.0</patient-db.version>
<pave.version>1.7</pave.version>
<peach.version>2.0</peach.version>
<purple.version>4.1</purple.version>
<redux.version>1.0</redux.version>
<sage.version>4.0</sage.version>
<sigs.version>1.2.1</sigs.version>
<sv-tools.version>1.0</sv-tools.version>
<teal.version>1.3.2</teal.version>
<virus-interpreter.version>3.7</virus-interpreter.version>
<v-chord.version>0.1</v-chord.version>
<wisp.version>1.2</wisp.version>
<commons.cli.version>1.3.1</commons.cli.version>
<immutables.version>2.9.3</immutables.version>
<htsjdk.version>2.23.0</htsjdk.version>
<intellij.annotations.version>12.0</intellij.annotations.version>
<google.guava.version>31.0.1-jre</google.guava.version>
<google.gson.version>2.8.9</google.gson.version>
<apache.commons.lang3.version>3.6</apache.commons.lang3.version>
<apache.commons.math3.version>3.6</apache.commons.math3.version>
<apache.commons.csv.version>1.9.0</apache.commons.csv.version>
<apache.commons.dbcp2.version>2.1.1</apache.commons.dbcp2.version>
<apache.log4j.version>2.17.1</apache.log4j.version>
<jooq.version>3.15.5</jooq.version>
<mysqlconnector.version>8.0.16</mysqlconnector.version>
<bouncycastle.jdk15.version>1.53</bouncycastle.jdk15.version>
<kotlin.version>1.5.32</kotlin.version>
<kotlin.coroutines.version>1.5.2</kotlin.coroutines.version>
<selenium.version>3.14.0</selenium.version>
<itext.version>7.1.5</itext.version>
<tablesaw.version>0.43.1</tablesaw.version>
<jcommander.version>1.81</jcommander.version>
<kotest.version>4.6.4</kotest.version>
<junit.version>4.13.1</junit.version>
<mockito.version>2.23.4</mockito.version>
<maven.compiler.source>${java.version}</maven.compiler.source>
<maven.compiler.target>${java.version}</maven.compiler.target>
<kotlin.compiler.jvmTarget>${java.version}</kotlin.compiler.jvmTarget>
</properties>
<build>
<extensions>
<extension>
<groupId>com.google.cloud.artifactregistry</groupId>
<artifactId>artifactregistry-maven-wagon</artifactId>
<version>2.2.0</version>
</extension>
</extensions>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>${maven.exec.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>${maven.compiler.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>${maven.assembly.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>${maven.jar.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>${maven.site.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
<version>${maven.surefire.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${maven.shade.plugin.version}</version>
</plugin>
<plugin>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-maven-plugin</artifactId>
<version>${kotlin.version}</version>
</plugin>
<plugin>
<groupId>org.jooq</groupId>
<artifactId>jooq-codegen-maven</artifactId>
<version>${jooq.version}</version>
</plugin>
</plugins>
</pluginManagement>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
</plugin>
</plugins>
</reporting>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>com.hartwig</groupId>
<artifactId>hmf-common</artifactId>
<version>${hmf-common.version}</version>
</dependency>
<dependency>
<groupId>com.hartwig</groupId>
<artifactId>patient-db</artifactId>
<version>${patient-db.version}</version>
</dependency>
<dependency>
<groupId>com.hartwig</groupId>
<artifactId>orange-datamodel</artifactId>
<version>${orange-datamodel.version}</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>${htsjdk.version}</version>
</dependency>
<dependency>
<groupId>com.intellij</groupId>
<artifactId>annotations</artifactId>
<version>${intellij.annotations.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${google.guava.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${google.gson.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons.cli.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${apache.commons.lang3.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>${apache.commons.math3.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>${apache.commons.csv.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-dbcp2</artifactId>
<version>${apache.commons.dbcp2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${apache.log4j.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<version>${apache.log4j.version}</version>
</dependency>
<dependency>
<groupId>org.jooq</groupId>
<artifactId>jooq</artifactId>
<version>${jooq.version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>${mysqlconnector.version}</version>
</dependency>
<dependency>
<groupId>org.immutables</groupId>
<artifactId>value</artifactId>
<version>${immutables.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.immutables</groupId>
<artifactId>gson</artifactId>
<version>${immutables.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.bouncycastle</groupId>
<artifactId>bcprov-jdk15on</artifactId>
<version>${bouncycastle.jdk15.version}</version>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-stdlib-jdk8</artifactId>
<version>${kotlin.version}</version>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-reflect</artifactId>
<version>${kotlin.version}</version>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlinx</groupId>
<artifactId>kotlinx-coroutines-core</artifactId>
<version>${kotlin.coroutines.version}</version>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-java</artifactId>
<version>${selenium.version}</version>
</dependency>
<dependency>
<groupId>com.itextpdf</groupId>
<artifactId>kernel</artifactId>
<version>${itext.version}</version>
</dependency>
<dependency>
<groupId>com.itextpdf</groupId>
<artifactId>layout</artifactId>
<version>${itext.version}</version>
</dependency>
<dependency>
<groupId>com.itextpdf</groupId>
<artifactId>io</artifactId>
<version>${itext.version}</version>
</dependency>
<dependency>
<groupId>tech.tablesaw</groupId>
<artifactId>tablesaw-core</artifactId>
<version>${tablesaw.version}</version>
</dependency>
<dependency>
<groupId>com.beust</groupId>
<artifactId>jcommander</artifactId>
<version>${jcommander.version}</version>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>com.hartwig</groupId>
<artifactId>hmf-common</artifactId>
<version>${hmf-common.version}</version>
<scope>test</scope>
<type>test-jar</type>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-test-junit</artifactId>
<version>${kotlin.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.kotest</groupId>
<artifactId>kotest-runner-junit5-jvm</artifactId>
<version>${kotest.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.kotest</groupId>
<artifactId>kotest-assertions-core-jvm</artifactId>
<version>${kotest.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
</dependencyManagement>
<distributionManagement>
<snapshotRepository>
<id>artifact-registry</id>
<url>artifactregistry://europe-west4-maven.pkg.dev/hmf-build/hmf-maven</url>
</snapshotRepository>
<repository>
<id>artifact-registry</id>
<url>artifactregistry://europe-west4-maven.pkg.dev/hmf-build/hmf-maven</url>
</repository>
</distributionManagement>
</project>