opencga
Used in:
components
- OverviewOverview
- VersionsVersions
- DependentsDependents
- DependenciesDependencies
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga</artifactId>
<version>4.0.0</version>
</dependency><?xml version="1.0" encoding="UTF-8"?>
<!--
~ Copyright 2015-2017 OpenCB
~
~ Licensed under the Apache License, Version 2.0 (the "License");
~ you may not use this file except in compliance with the License.
~ You may obtain a copy of the License at
~
~ http://www.apache.org/licenses/LICENSE-2.0
~
~ Unless required by applicable law or agreed to in writing, software
~ distributed under the License is distributed on an "AS IS" BASIS,
~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
~ See the License for the specific language governing permissions and
~ limitations under the License.
-->
<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://maven.apache.org/POM/4.0.0"
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.opencb.opencga</groupId>
<artifactId>opencga</artifactId>
<version>4.0.0</version>
<packaging>pom</packaging>
<name>OpenCGA</name>
<description>OpenCGA projects implements a big data platform for genomic data analysis</description>
<url>http://docs.opencb.org/display/opencga/</url>
<modules>
<module>opencga-core</module>
<module>opencga-app</module>
<module>opencga-catalog</module>
<module>opencga-master</module>
<module>opencga-analysis</module>
<module>opencga-storage</module>
<module>opencga-client</module>
<module>opencga-server</module>
<module>opencga-clinical</module>
<module>opencga-test</module>
</modules>
<properties>
<pyopencga.version>4.0.0</pyopencga.version>
<opencgar.version>4.0.0</opencgar.version>
<cellbase.version>7.0.0</cellbase.version>
<biodata.version>4.0.0</biodata.version>
<java-common-libs.version>6.0.0</java-common-libs.version>
<iva.version>4.0.0</iva.version>
<oskar.version>0.2.0</oskar.version>
<jackson.version>2.14.3</jackson.version>
<jersey.version>2.30.1</jersey.version>
<collections.version>4.4</collections.version>
<avro.version>1.7.7</avro.version>
<protobuf.version>3.11.4</protobuf.version>
<grpc.version>1.28.1</grpc.version>
<slf4j.version>1.7.36</slf4j.version>
<log4j2.version>2.17.2</log4j2.version>
<solr.version>8.11.3</solr.version>
<jjwt.version>0.11.2</jjwt.version>
<!-- <jetty.version>9.4.17.v20190418</jetty.version>-->
<jetty.version>9.4.53.v20231009</jetty.version>
<jetty-for-hadoop-test.version>${jetty.version}</jetty-for-hadoop-test.version>
<guava.version>28.0-jre</guava.version>
<htsjdk.version>2.23.0</htsjdk.version>
<snpeff.version>4.3.1</snpeff.version>
<mongodb-driver.version>4.11.4</mongodb-driver.version>
<commons-io.version>2.8.0</commons-io.version>
<commons-lang3.version>3.14.0</commons-lang3.version>
<commons-codec.version>1.7</commons-codec.version>
<reflections.version>0.9.10</reflections.version>
<mockito.version>2.2.27</mockito.version>
<findbugs-annotations.version>2.0.1</findbugs-annotations.version>
<junit.version>4.13.2</junit.version>
<jline.version>3.12.1</jline.version>
<javax-mail.version>1.4.7</javax-mail.version>
<hamcrest-core.version>1.3</hamcrest-core.version>
<ga4gh.version>0.6.0a5</ga4gh.version>
<jansi.version>2.4.0</jansi.version>
<jakarta.ws.rs-api.version>2.1.6</jakarta.ws.rs-api.version>
<jcommander.version>1.69</jcommander.version>
<jackson-codehaus.version>1.9.13</jackson-codehaus.version>
<adal4j.version>1.6.3</adal4j.version>
<microsoft-graph.version>1.4.0</microsoft-graph.version>
<json-smart.version>2.3</json-smart.version>
<gson.version>2.8.0</gson.version>
<nimbus-jose-jwt.version>9.31</nimbus-jose-jwt.version>
<azure-client.version>1.7.14</azure-client.version>
<azure-batch.version>4.0.1</azure-batch.version>
<!-- Cannot upgrade the version until we upgrade GRPC version -->
<azure.version>1.13.0</azure.version>
<azure.optional>true</azure.optional>
<azure-storage-blob.version>11.0.0</azure-storage-blob.version>
<httpclient.version>4.5.6</httpclient.version>
<oauth2-oidc-sdk.version>5.64.4</oauth2-oidc-sdk.version>
<passay.version>1.6.1</passay.version>
<kubernetes.version>6.13.1</kubernetes.version>
<javax.servlet-api.version>3.1.0</javax.servlet-api.version>
<ant.version>1.10.12</ant.version>
<httpcore.version>4.4.13</httpcore.version>
<log4j.version>1.2.17</log4j.version>
<javax.ws.rs-api.version>2.0.1</javax.ws.rs-api.version>
<jmeter.version>5.0</jmeter.version>
<ApacheJMeter_components.version>5.0</ApacheJMeter_components.version>
<grep4j.version>1.8.7</grep4j.version>
<redisson.version>2.2.0</redisson.version>
<jsr305.version>3.0.2</jsr305.version>
<commons-compress.version>1.4.1</commons-compress.version>
<rxjava.version>2.2.0</rxjava.version>
<client-runtime.version>2.1.0</client-runtime.version>
<reactive-streams.version>1.0.0</reactive-streams.version>
<snappy-java.version>1.1.10.4</snappy-java.version>
<parquet-avro.version>${parquet-common.version}</parquet-avro.version>
<jorphan.version>5.0</jorphan.version>
<opencga.war.name>opencga</opencga.war.name>
<opencga.env.file>opencga-env.sh</opencga.env.file>
<opencga.hadoop.thirdparty.version>1.0.0-SNAPSHOT</opencga.hadoop.thirdparty.version>
<opencga-hadoop-shaded.id.default>hdp3.1</opencga-hadoop-shaded.id.default>
<opencga-hadoop-shaded.id>${opencga-hadoop-shaded.id.default}</opencga-hadoop-shaded.id>
<opencga-hadoop-lib.artifactId>opencga-storage-hadoop-lib-${opencga-hadoop-shaded.id}</opencga-hadoop-lib.artifactId>
<opencga-hadoop-shaded.artifactId>opencga-hadoop-shaded-${opencga-hadoop-shaded.id}</opencga-hadoop-shaded.artifactId>
<opencga-storage-hadoop-compat.id-default>hbase2.0</opencga-storage-hadoop-compat.id-default>
<opencga-storage-hadoop-compat.id>${opencga-storage-hadoop-compat.id-default}</opencga-storage-hadoop-compat.id>
<sonar.organization>opencb</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
<!-- This prevents findbugs plugin to check all the dependency locations -->
<dependency.locations.enabled>false</dependency.locations.enabled>
<maven.compiler.source>1.8</maven.compiler.source>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<surefire.skipDefaultTestExecution>false</surefire.skipDefaultTestExecution>
<surefire.testFailureIgnore>false</surefire.testFailureIgnore>
<maven-surefire-plugin.version>3.1.0</maven-surefire-plugin.version>
<parquet-hadoop.version>${parquet-common.version}</parquet-hadoop.version>
<parquet-common.version>1.7.0</parquet-common.version>
<commons-logging.version>1.1.3</commons-logging.version>
<jcl-over-slf4j.version>1.7.24</jcl-over-slf4j.version>
<servlet-api.version>2.5-20081211</servlet-api.version>
<!--TO REMOVE:
The version of Java (11.0.21) used to run this analysis is deprecated, and SonarCloud no longer supports it. Please upgrade to Java 17 or later.
As a temporary measure, you can set the property 'sonar.scanner.force-deprecated-java-version' to 'true' to continue using Java 11.0.21
This workaround will only be effective until January 28, 2024. After this date, all scans using the deprecated Java 11 will fail.
-->
<sonar.scanner.force-deprecated-java-version>true</sonar.scanner.force-deprecated-java-version>
<kryo.version>2.23.0</kryo.version>
<lombok.version>1.18.30</lombok.version>
<maven-war-plugin.version>3.4.0</maven-war-plugin.version>
</properties>
<scm>
<url>https://github.com/opencb/opencga</url>
<connection>scm:git:git://github.com/opencb/opencga.git</connection>
<developerConnection>scm:git:git@github.com:opencb/opencga.git</developerConnection>
</scm>
<licenses>
<license>
<name>Apache License, Version 2</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
</license>
</licenses>
<developers>
<developer>
<id>imedina</id>
<name>Nacho</name>
<email>igmecas@gmail.com</email>
</developer>
<developer>
<id>j-coll</id>
<name>Jacobo</name>
<email>jacobo167@gmail.com</email>
</developer>
<developer>
<id>pfurio</id>
<name>Pedro</name>
<email>pedrofurio@gmail.com</email>
</developer>
<developer>
<id>jtarraga</id>
<name>Joaquin</name>
<email>joaquintarraga@gmail.com</email>
</developer>
<developer>
<id>juanfeSanahuja</id>
<name>Juanfe</name>
<email>juanfesanahuja@gmail.com</email>
</developer>
</developers>
<mailingLists>
<mailingList>
<name>OpenCB Mailing List</name>
<archive>https://groups.google.com/forum/#!forum/opencb</archive>
<post>opencb@googlegroups.com</post>
</mailingList>
</mailingLists>
<repositories>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
<snapshots>
<enabled>true</enabled>
<updatePolicy>daily</updatePolicy>
</snapshots>
</repository>
<repository>
<id>github</id>
<url>https://maven.pkg.github.com/opencb</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
<dependencyManagement>
<dependencies>
<!-- Intra-module dependencies -->
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-analysis</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-master</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-client</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-app</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-hadoop-${opencga-hadoop-shaded.id.default}</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-test</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-hadoop-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-hadoop-core</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-core</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-catalog</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-analysis</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
</dependency>
<dependency>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-server</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>org.opencb.opencga</groupId>
<artifactId>opencga-storage-hadoop-${opencga-hadoop-shaded.id.default}</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- OpenCB dependencies -->
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-mongodb</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-solr</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
<version>${biodata.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
<version>${biodata.version}</version>
<exclusions>
<exclusion>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-lite</artifactId>
</exclusion>
<exclusion>
<groupId>org.mortbay.jetty</groupId>
<artifactId>servlet-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.mortbay.jetty</groupId>
<artifactId>servlet-api</artifactId>
<version>${servlet-api.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-tools</artifactId>
<version>${biodata.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.avro</groupId>
<artifactId>avro-ipc</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-core</artifactId>
<version>${cellbase.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.cellbase</groupId>
<artifactId>cellbase-client</artifactId>
<version>${cellbase.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.opencb.oskar</groupId>
<artifactId>oskar-analysis</artifactId>
<version>${oskar.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- General dependencies -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>${collections.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${commons-lang3.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>${commons-codec.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<version>${log4j2.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.datatype</groupId>
<artifactId>jackson-datatype-joda</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-yaml</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-xml</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
<artifactId>jackson-dataformat-cbor</artifactId>
<version>${jackson.version}</version>
</dependency>
<dependency>
<groupId>org.apache.jmeter</groupId>
<artifactId>ApacheJMeter_components</artifactId>
<version>${ApacheJMeter_components.version}</version>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-solrj</artifactId>
<version>${solr.version}</version>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-core</artifactId>
<version>${solr.version}</version>
</dependency>
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-test-framework</artifactId>
<version>${solr.version}</version>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-web</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.jmeter</groupId>
<artifactId>ApacheJMeter_core</artifactId>
<version>${jmeter.version}</version>
<exclusions>
<exclusion>
<artifactId>mongo-java-driver</artifactId>
<groupId>org.mongodb</groupId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</exclusion>
<exclusion>
<groupId>com.beust</groupId>
<artifactId>jcommander</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.jmeter</groupId>
<artifactId>ApacheJMeter_http</artifactId>
<version>${jmeter.version}</version>
<exclusions>
<exclusion>
<artifactId>mongo-java-driver</artifactId>
<groupId>org.mongodb</groupId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.jmeter</groupId>
<artifactId>ApacheJMeter_java</artifactId>
<version>${jmeter.version}</version>
<exclusions>
<exclusion>
<artifactId>mongo-java-driver</artifactId>
<groupId>org.mongodb</groupId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.jmeter</groupId>
<artifactId>jorphan</artifactId>
<version>${jorphan.version}</version>
</dependency>
<dependency>
<groupId>javax.ws.rs</groupId>
<artifactId>javax.ws.rs-api</artifactId>
<version>${javax.ws.rs-api.version}</version>
</dependency>
<dependency>
<groupId>org.jline</groupId>
<artifactId>jline-reader</artifactId>
<version>${jline.version}</version>
</dependency>
<dependency>
<groupId>org.jline</groupId>
<artifactId>jline-terminal</artifactId>
<version>${jline.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-http</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-io</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util-ajax</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-xml</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-rewrite</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-security</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-client</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-project</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-alpn-client</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-alpn-java-client</artifactId>
<version>${jetty.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-common</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-server</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet-core</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.inject</groupId>
<artifactId>jersey-hk2</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-json-jackson</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-multipart</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-jaxb</artifactId>
<version>${jersey.version}</version>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-api</artifactId>
<version>${jjwt.version}</version>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-impl</artifactId>
<version>${jjwt.version}</version>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-jackson</artifactId>
<version>${jjwt.version}</version>
</dependency>
<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>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
<version>${findbugs-annotations.version}</version>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
<version>${grpc.version}</version>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-api</artifactId>
<version>${grpc.version}</version>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-protobuf</artifactId>
<version>${grpc.version}</version>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-stub</artifactId>
<version>${grpc.version}</version>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
<version>${avro.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro-ipc</artifactId>
<version>${avro.version}</version>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro-mapred</artifactId>
<version>${avro.version}</version>
<classifier>hadoop2</classifier>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongodb-driver-core</artifactId>
<version>${mongodb-driver.version}</version>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongodb-driver-sync</artifactId>
<version>${mongodb-driver.version}</version>
</dependency>
<dependency>
<groupId>org.apache.parquet</groupId>
<artifactId>parquet-common</artifactId>
<version>${parquet-common.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${jcl-over-slf4j.version}</version>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>bson</artifactId>
<version>${mongodb-driver.version}</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>${commons-logging.version}</version>
</dependency>
<dependency>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
<version>${javax-mail.version}</version>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>${reflections.version}</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>${htsjdk.version}</version>
</dependency>
<dependency>
<groupId>com.databricks</groupId>
<artifactId>SnpEff</artifactId>
<version>${snpeff.version}</version>
<exclusions>
<exclusion>
<groupId>distlib</groupId>
<artifactId>distlib</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.parquet</groupId>
<artifactId>parquet-avro</artifactId>
<version>${parquet-avro.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<version>${hamcrest-core.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.ga4gh</groupId>
<artifactId>ga4gh</artifactId>
<version>${ga4gh.version}</version>
</dependency>
<dependency>
<groupId>org.fusesource.jansi</groupId>
<artifactId>jansi</artifactId>
<version>${jansi.version}</version>
</dependency>
<dependency>
<groupId>jakarta.ws.rs</groupId>
<artifactId>jakarta.ws.rs-api</artifactId>
<version>${jakarta.ws.rs-api.version}</version>
</dependency>
<dependency>
<groupId>com.beust</groupId>
<artifactId>jcommander</artifactId>
<version>${jcommander.version}</version>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>adal4j</artifactId>
<version>${adal4j.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.microsoft.graph</groupId>
<artifactId>microsoft-graph</artifactId>
<version>${microsoft-graph.version}</version>
</dependency>
<dependency>
<groupId>net.minidev</groupId>
<artifactId>json-smart</artifactId>
<version>${json-smart.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${gson.version}</version>
</dependency>
<dependency>
<groupId>com.nimbusds</groupId>
<artifactId>nimbus-jose-jwt</artifactId>
<version>${nimbus-jose-jwt.version}</version>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-client-runtime</artifactId>
<version>${azure-client.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-client-authentication</artifactId>
<version>${azure-client.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>${httpclient.version}</version>
</dependency>
<dependency>
<groupId>com.nimbusds</groupId>
<artifactId>oauth2-oidc-sdk</artifactId>
<version>${oauth2-oidc-sdk.version}</version>
</dependency>
<dependency>
<groupId>org.passay</groupId>
<artifactId>passay</artifactId>
<version>${passay.version}</version>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-batch</artifactId>
<version>${azure-batch.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>io.fabric8</groupId>
<artifactId>kubernetes-client</artifactId>
<version>${kubernetes.version}</version>
</dependency>
<dependency>
<groupId>io.fabric8</groupId>
<artifactId>kubernetes-model</artifactId>
<version>${kubernetes.version}</version>
</dependency>
<dependency>
<groupId>io.fabric8</groupId>
<artifactId>kubernetes-model-core</artifactId>
<version>${kubernetes.version}</version>
</dependency>
<dependency>
<groupId>io.fabric8</groupId>
<artifactId>kubernetes-client-api</artifactId>
<version>${kubernetes.version}</version>
</dependency>
<dependency>
<groupId>io.fabric8</groupId>
<artifactId>kubernetes-model-batch</artifactId>
<version>${kubernetes.version}</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<version>${javax.servlet-api.version}</version>
</dependency>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>${ant.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
<version>${httpcore.version}</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>${log4j.version}</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
<version>${jackson-codehaus.version}</version>
</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.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<type>maven-plugin</type>
</dependency>
<dependency>
<groupId>com.googlecode.grep4j</groupId>
<artifactId>grep4j</artifactId>
<version>${grep4j.version}</version>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>${lombok.version}</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.redisson</groupId>
<artifactId>redisson</artifactId>
<version>${redisson.version}</version>
<exclusions>
<exclusion>
<groupId>io.netty</groupId>
<artifactId>netty-codec</artifactId>
</exclusion>
<exclusion>
<groupId>io.netty</groupId>
<artifactId>netty-common</artifactId>
</exclusion>
<exclusion>
<groupId>io.netty</groupId>
<artifactId>netty-handler</artifactId>
</exclusion>
<exclusion>
<groupId>io.netty</groupId>
<artifactId>netty-buffer</artifactId>
</exclusion>
<exclusion>
<groupId>io.netty</groupId>
<artifactId>netty-transport</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.reactivestreams</groupId>
<artifactId>reactive-streams</artifactId>
<version>${reactive-streams.version}</version>
</dependency>
<dependency>
<groupId>com.microsoft.rest.v2</groupId>
<artifactId>client-runtime</artifactId>
<version>${client-runtime.version}</version>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure-storage-blob</artifactId>
<version>${azure-storage-blob.version}</version>
<optional>${azure.optional}</optional>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>${jsr305.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>${commons-compress.version}</version>
</dependency>
<dependency>
<groupId>io.reactivex.rxjava2</groupId>
<artifactId>rxjava</artifactId>
<version>${rxjava.version}</version>
</dependency>
<dependency>
<groupId>org.xerial.snappy</groupId>
<artifactId>snappy-java</artifactId>
<version>${snappy-java.version}</version>
</dependency>
<dependency>
<groupId>org.apache.parquet</groupId>
<artifactId>parquet-hadoop</artifactId>
<version>${parquet-hadoop.version}</version>
</dependency>
<dependency>
<groupId>org.jline</groupId>
<artifactId>jline-terminal-jna</artifactId>
<version>${jline.version}</version>
</dependency>
<dependency>
<groupId>com.microsoft.azure</groupId>
<artifactId>azure</artifactId>
<version>${azure.version}</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
<version>${kryo.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/test/java</testSourceDirectory>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.5.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>${maven-war-plugin.version}</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.10.1</version>
<configuration>
<source>${maven.compiler.source}</source>
<target>${maven.compiler.source}</target>
<showDeprecation>true</showDeprecation>
<showWarnings>true</showWarnings>
<meminitial>128m</meminitial>
<maxmem>512m</maxmem>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.17</version>
<dependencies>
<dependency>
<groupId>com.puppycrawl.tools</groupId>
<artifactId>checkstyle</artifactId>
<version>8.1</version>
</dependency>
</dependencies>
<configuration>
<configLocation>checkstyle.xml</configLocation>
<excludes>
org/opencb/opencga/core/**,
org/opencb/opencga/app/**,
org/opencb/opencga/analysis/**,
org/opencb/opencga/server/**,
org/opencb/opencga/test/**,
org/opencb/opencga/storage/app/**,
org/opencb/opencga/client/rest/clients/**,
org/opencb/opencga/storage/alignment/**,
org/opencb/opencga/storage/variant/**,
org/opencb/opencga/storage/datamanagers/**,
org/opencb/opencga/storage/hadoop/variant/models/protobuf/**,
org/opencb/opencga/storage/server/grpc/**,
</excludes>
<resourceExcludes>
benchmark/jmeter/**
</resourceExcludes>
</configuration>
<executions>
<execution>
<id>validate</id>
<phase>validate</phase>
<configuration>
<configLocation>checkstyle.xml</configLocation>
</configuration>
<goals>
<goal>check</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.9.1</version>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.8</version>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>default-report</id>
<goals>
<goal>report</goal>
</goals>
</execution>
<execution>
<id>default-check</id>
<goals>
<goal>check</goal>
</goals>
<configuration>
<rules>
<!-- <rule>-->
<!-- <element>BUNDLE</element>-->
<!-- <limits>-->
<!-- <limit>-->
<!-- <counter>COMPLEXITY</counter>-->
<!-- <value>COVEREDRATIO</value>-->
<!-- <minimum>0.60</minimum>-->
<!-- </limit>-->
<!-- </limits>-->
<!-- </rule>-->
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<executions>
<execution>
<id>default-test</id>
<configuration>
<skip>${surefire.skipDefaultTestExecution}</skip>
<forkCount>1</forkCount>
<reuseForks>false</reuseForks>
<!--<argLine>-Xmx1024m -XX:MaxPermSize=256m</argLine>-->
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.6.0</version>
<executions>
<execution>
<id>analyze</id>
<goals>
<goal>analyze-only</goal>
</goals>
<configuration>
<failOnWarning>true</failOnWarning>
<ignoredUnusedDeclaredDependencies>
<ignoredUnusedDeclaredDependency>*</ignoredUnusedDeclaredDependency>
</ignoredUnusedDeclaredDependencies>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>2.9</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
</plugin>
<plugin>
<groupId>com.github.spotbugs</groupId>
<artifactId>spotbugs-maven-plugin</artifactId>
<version>3.1.12.2</version>
</plugin>
</plugins>
</reporting>
<profiles>
<profile>
<id>prod-war</id>
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<properties>
<opencga.war.name>opencga</opencga.war.name>
</properties>
</profile>
<profile>
<id>default-config</id>
<activation>
<!-- Do not use "activeByDefault" as it might get deactivated when using any hadoop profile -->
<property>
<name>!skipDefaultConfig</name>
</property>
</activation>
<properties>
<opencga.war.name>opencga-${project.parent.version}</opencga.war.name>
<!-- General -->
<OPENCGA.INSTALLATION.DIR>/opt/opencga</OPENCGA.INSTALLATION.DIR>
<OPENCGA.USER.WORKSPACE>/opt/opencga/sessions</OPENCGA.USER.WORKSPACE>
<OPENCGA.ANALYSIS.SCRATCH.DIR></OPENCGA.ANALYSIS.SCRATCH.DIR>
<OPENCGA.DB.PREFIX>opencga</OPENCGA.DB.PREFIX>
<OPENCGA.EXECUTION.MODE>LOCAL</OPENCGA.EXECUTION.MODE>
<OPENCGA.ACCOUNT.MAX_LOGIN_ATTEMPTS>5</OPENCGA.ACCOUNT.MAX_LOGIN_ATTEMPTS>
<!-- Client -->
<OPENCGA.CLIENT.REST.HOST>https://ws.opencb.org/opencga-prod</OPENCGA.CLIENT.REST.HOST>
<OPENCGA.CLIENT.GRPC.HOST>localhost:9091</OPENCGA.CLIENT.GRPC.HOST>
<OPENCGA.SERVER.REST.PORT>9090</OPENCGA.SERVER.REST.PORT>
<OPENCGA.SERVER.GRPC.PORT>9091</OPENCGA.SERVER.GRPC.PORT>
<OPENCGA.MONITOR.PORT>9092</OPENCGA.MONITOR.PORT>
<!-- Catalog -->
<OPENCGA.CATALOG.DB.HOSTS>localhost:27017</OPENCGA.CATALOG.DB.HOSTS>
<OPENCGA.CATALOG.DB.USER></OPENCGA.CATALOG.DB.USER>
<OPENCGA.CATALOG.DB.PASSWORD></OPENCGA.CATALOG.DB.PASSWORD>
<OPENCGA.CATALOG.DB.AUTHENTICATION_DATABASE></OPENCGA.CATALOG.DB.AUTHENTICATION_DATABASE>
<OPENCGA.CATALOG.DB.CONNECTIONS_PER_HOST>20</OPENCGA.CATALOG.DB.CONNECTIONS_PER_HOST>
<!-- Storage -->
<OPENCGA.STORAGE.DEFAULT_ENGINE>hadoop</OPENCGA.STORAGE.DEFAULT_ENGINE>
<OPENCGA.STORAGE.CACHE.HOST>localhost:6379</OPENCGA.STORAGE.CACHE.HOST>
<!-- Storage Variants general -->
<OPENCGA.STORAGE.VARIANT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.VARIANT.DB.HOSTS>
<OPENCGA.STORAGE.VARIANT.DB.USER></OPENCGA.STORAGE.VARIANT.DB.USER>
<OPENCGA.STORAGE.VARIANT.DB.PASSWORD></OPENCGA.STORAGE.VARIANT.DB.PASSWORD>
<OPENCGA.STORAGE.SEARCH.HOST>http://localhost:8983/solr/</OPENCGA.STORAGE.SEARCH.HOST>
<OPENCGA.STORAGE.SEARCH.CONFIG_SET>opencga-variant-configset-${project.parent.version}
</OPENCGA.STORAGE.SEARCH.CONFIG_SET>
<OPENCGA.STORAGE.SEARCH.TIMEOUT>30000</OPENCGA.STORAGE.SEARCH.TIMEOUT>
<OPENCGA.STORAGE.CLINICAL.HOST>http://localhost:8983/solr/</OPENCGA.STORAGE.CLINICAL.HOST>
<OPENCGA.STORAGE.CLINICAL.MANAGER>""</OPENCGA.STORAGE.CLINICAL.MANAGER>
<OPENCGA.STORAGE.CLINICAL.TIMEOUT>30000</OPENCGA.STORAGE.CLINICAL.TIMEOUT>
<OPENCGA.STORAGE.RGA.HOST>http://localhost:8983/solr/</OPENCGA.STORAGE.RGA.HOST>
<OPENCGA.STORAGE.RGA.CONFIG_SET>opencga-rga-configset-${project.parent.version}
</OPENCGA.STORAGE.RGA.CONFIG_SET>
<OPENCGA.STORAGE.RGA.TIMEOUT>30000</OPENCGA.STORAGE.RGA.TIMEOUT>
<!-- Storage Alignments general -->
<OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>localhost:27017</OPENCGA.STORAGE.ALIGNMENT.DB.HOSTS>
<OPENCGA.STORAGE.ALIGNMENT.DB.USER></OPENCGA.STORAGE.ALIGNMENT.DB.USER>
<OPENCGA.STORAGE.ALIGNMENT.DB.PASSWORD></OPENCGA.STORAGE.ALIGNMENT.DB.PASSWORD>
<!-- Storage-mongodb -->
<OPENCGA.STORAGE.MONGODB.VARIANT.DB.AUTHENTICATION_DATABASE></OPENCGA.STORAGE.MONGODB.VARIANT.DB.AUTHENTICATION_DATABASE>
<OPENCGA.STORAGE.MONGODB.VARIANT.DB.CONNECTIONS_PER_HOST>20
</OPENCGA.STORAGE.MONGODB.VARIANT.DB.CONNECTIONS_PER_HOST>
<!-- Storage-hadoop -->
<OPENCGA.STORAGE.HADOOP.VARIANT.DB.USER></OPENCGA.STORAGE.HADOOP.VARIANT.DB.USER>
<OPENCGA.STORAGE.HADOOP.VARIANT.DB.PASSWORD></OPENCGA.STORAGE.HADOOP.VARIANT.DB.PASSWORD>
<OPENCGA.STORAGE.HADOOP.VARIANT.HBASE.NAMESPACE></OPENCGA.STORAGE.HADOOP.VARIANT.HBASE.NAMESPACE>
<!-- Email server -->
<OPENCGA.MAIL.HOST></OPENCGA.MAIL.HOST>
<OPENCGA.MAIL.PORT></OPENCGA.MAIL.PORT>
<OPENCGA.MAIL.USER></OPENCGA.MAIL.USER>
<OPENCGA.MAIL.PASSWORD></OPENCGA.MAIL.PASSWORD>
<!-- cellbase -->
<OPENCGA.CELLBASE.REST.HOST>https://uk.ws.zettagenomics.com/cellbase/</OPENCGA.CELLBASE.REST.HOST>
<OPENCGA.CELLBASE.VERSION>v5.8</OPENCGA.CELLBASE.VERSION>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>deploy-maven</id>
<distributionManagement>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
<snapshotRepository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
</distributionManagement>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.3.2</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
<configuration>
<doclint>none</doclint>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>deploy</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<!-- Prevent `gpg` from using pinentry programs -->
<gpgArguments>
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.8</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>deploy-github</id>
<distributionManagement>
<repository>
<id>github</id>
<name>GitHub OpenCB Apache Maven Packages</name>
<url>https://maven.pkg.github.com/opencb/opencga</url>
</repository>
</distributionManagement>
<build>
</build>
</profile>
<profile>
<id>hdp3.1</id>
<activation>
<property>
<name>hadoop</name>
<value>hdp3.1</value>
</property>
</activation>
<properties>
<opencga-hadoop-shaded.id>hdp3.1</opencga-hadoop-shaded.id>
<opencga-storage-hadoop-compat.id>hbase2.0</opencga-storage-hadoop-compat.id>
<jetty-for-hadoop-test.version>9.3.25.v20180904</jetty-for-hadoop-test.version>
</properties>
</profile>
<profile>
<id>hdi5.1</id>
<activation>
<property>
<name>hadoop</name>
<value>hdi5.1</value>
</property>
</activation>
<properties>
<opencga-hadoop-shaded.id>hdi5.1</opencga-hadoop-shaded.id>
<opencga-storage-hadoop-compat.id>hbase2.4</opencga-storage-hadoop-compat.id>
</properties>
</profile>
<profile>
<id>emr6.1</id>
<activation>
<property>
<name>hadoop</name>
<value>emr6.1</value>
</property>
</activation>
<properties>
<opencga-hadoop-shaded.id>emr6.1</opencga-hadoop-shaded.id>
<opencga-storage-hadoop-compat.id>hbase2.2</opencga-storage-hadoop-compat.id>
<!-- AWS changes the version of Jetty in their custom jar -->
<jetty-for-hadoop-test.version>9.4.20.v20190813</jetty-for-hadoop-test.version>
</properties>
</profile>
<profile>
<id>emr6.13</id>
<activation>
<property>
<name>hadoop</name>
<value>emr6.13</value>
</property>
</activation>
<properties>
<opencga-hadoop-shaded.id>emr6.13</opencga-hadoop-shaded.id>
<opencga-storage-hadoop-compat.id>hbase2.4</opencga-storage-hadoop-compat.id>
</properties>
</profile>
<profile>
<id>runShortTests</id>
<properties>
<surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<executions>
<execution>
<id>shortTestsExecution</id>
<phase>test</phase>
<goals>
<goal>test</goal>
</goals>
<configuration>
<testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
<reuseForks>true</reuseForks>
<forkCount>5</forkCount>
<groups>org.opencb.opencga.core.testclassification.duration.ShortTests</groups>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>runMediumTests</id>
<properties>
<surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<executions>
<execution>
<id>mediumTestsExecution</id>
<phase>test</phase>
<goals>
<goal>test</goal>
</goals>
<configuration>
<testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
<!-- <reuseForks>true</reuseForks>-->
<reuseForks>false</reuseForks>
<forkCount>1</forkCount>
<groups>org.opencb.opencga.core.testclassification.duration.MediumTests</groups>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>runLongTests</id>
<properties>
<surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<executions>
<execution>
<id>longTestsExecution</id>
<phase>test</phase>
<goals>
<goal>test</goal>
</goals>
<configuration>
<testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
<reuseForks>false</reuseForks>
<forkCount>1</forkCount>
<groups>org.opencb.opencga.core.testclassification.duration.LongTests</groups>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>runUncategorizedTests</id>
<properties>
<surefire.skipDefaultTestExecution>true</surefire.skipDefaultTestExecution>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<executions>
<execution>
<id>uncategorizedTestsExecution</id>
<phase>test</phase>
<goals>
<goal>test</goal>
</goals>
<configuration>
<testFailureIgnore>${surefire.testFailureIgnore}</testFailureIgnore>
<reuseForks>false</reuseForks>
<forkCount>1</forkCount>
<excludedGroups>
org.opencb.opencga.core.testclassification.duration.ShortTests,org.opencb.opencga.core.testclassification.duration.MediumTests,org.opencb.opencga.core.testclassification.duration.LongTests
</excludedGroups>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>