biodata
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<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata</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="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.opencb.biodata</groupId>
<artifactId>biodata</artifactId>
<version>4.0.0</version>
<packaging>pom</packaging>
<name>Biodata</name>
<description>Biological entities and their equivalents in different file formats typically used in bioinformatics</description>
<url>https://github.com/opencb/biodata/wiki</url>
<modules>
<module>biodata-formats</module>
<module>biodata-models</module>
<module>biodata-tools</module>
<module>biodata-external</module>
</modules>
<properties>
<!-- All dependency versions must be defined here -->
<java-common-libs.version>6.0.0</java-common-libs.version>
<jackson.version>2.14.3</jackson.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>
<htsjdk.version>2.23.0</htsjdk.version>
<slf4j.version>1.7.36</slf4j.version>
<jsr.version>3.0.2</jsr.version>
<commons-lang.version>3.14.0</commons-lang.version>
<!-- <jackson-mapper.version>2.9.9</jackson-mapper.version>-->
<guava.version>19.0</guava.version>
<commons-io.version>2.12.0</commons-io.version>
<biojava-core.version>5.0.0</biojava-core.version>
<ga4gh.version>0.6.0a5</ga4gh.version>
<SnpEff.version>4.3.1</SnpEff.version>
<rocksdbjni.version>4.5.1</rocksdbjni.version>
<jakarta.xml.bind-api.version>2.3.3</jakarta.xml.bind-api.version>
<owlapi-oboformat.version>5.1.13</owlapi-oboformat.version>
<jaxb-impl.version>2.3.3</jaxb-impl.version>
<biojava-alignment.version>4.1.0</biojava-alignment.version>
<junit.version>4.13.2</junit.version>
<!-- Other properties -->
<sonar.organization>opencb</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
<maven.compiler.source>1.8</maven.compiler.source>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<log4j.version>1.2.17</log4j.version>
</properties>
<scm>
<url>https://github.com/opencb/biodata</url>
<connection>scm:git:git://github.com/opencb/biodata.git</connection>
<developerConnection>scm:git:git@github.com:opencb/biodata.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>javild</id>
<name>Javier</name>
<email>javild@gmail.com</email>
</developer>
<developer>
<id>julie-sullivan</id>
<name>Julie</name>
<email>julie.sullivan@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>
<!-- OpenCB dependencies -->
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-formats</artifactId>
<version>${project.parent.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.biodata</groupId>
<artifactId>biodata-models</artifactId>
<version>${project.parent.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-lib</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.commons</groupId>
<artifactId>commons-datastore-core</artifactId>
<version>${java-common-libs.version}</version>
</dependency>
<dependency>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>${jakarta.xml.bind-api.version}</version>
</dependency>
<dependency>
<groupId>org.rocksdb</groupId>
<artifactId>rocksdbjni</artifactId>
<version>${rocksdbjni.version}</version>
</dependency>
<dependency>
<groupId>org.opencb.ga4gh</groupId>
<artifactId>ga4gh</artifactId>
<version>${ga4gh.version}</version>
</dependency>
<dependency>
<groupId>org.rocksdb</groupId>
<artifactId>rocksdbjni</artifactId>
<version>${rocksdbjni.version}</version>
</dependency>
<dependency>
<groupId>com.databricks</groupId>
<artifactId>SnpEff</artifactId>
<version>${SnpEff.version}</version>
<exclusions>
<exclusion>
<groupId>distlib</groupId>
<artifactId>distlib</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>${htsjdk.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>${jackson.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>${commons-lang.version}</version>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
<version>${avro.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-collections4</artifactId>
<version>${collections.version}</version>
</dependency>
<dependency>
<groupId>com.google.protobuf</groupId>
<artifactId>protobuf-java</artifactId>
<version>${protobuf.version}</version>
</dependency>
<dependency>
<groupId>io.grpc</groupId>
<artifactId>grpc-all</artifactId>
<version>${grpc.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>${jsr.version}</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>${biojava-alignment.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>${biojava-core.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
<!-- Better use slf4j-simple instead of logj4 for testing, as it doesn't require any configuration -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>${slf4j.version}</version>
<scope>test</scope>
<optional>true</optional>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
<version>${jaxb-impl.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-oboformat</artifactId>
<version>${owlapi-oboformat.version}</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>${log4j.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
<build>
<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-surefire-plugin</artifactId>
<version>3.0.0-M7</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-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>
<ignoredNonTestScopedDependencies>
<ignoredNonTestScopedDependency>*</ignoredNonTestScopedDependency>
</ignoredNonTestScopedDependencies>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
<version>3.0.0-M8</version>
</plugin>
</plugins>
</reporting>
<profiles>
<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/biodata</url>
</repository>
</distributionManagement>
<build>
</build>
</profile>
</profiles>
</project>
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