pom.xml

<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>io.github.bigbio.pgatk</groupId>
  <artifactId>pgatk-io</artifactId>
  <version>1.0.1-SNAPSHOT</version>
  <packaging>jar</packaging>
  <name>pgatk-io</name>

  <description>The pgatk io is a library to handle proteogeomics file formats</description>
  <url>https://github.com/bigbio/pgatk-io</url>


  <developers>
    <developer>
      <id>jgriss</id>
      <name>Johannes Griss</name>
      <email>jgriss@ebi.ac.uk</email>
      <organization>Proteomics Services Team - EBI</organization>
      <organizationUrl>http://www.ebi.ac.uk/proteomics</organizationUrl>
      <timezone>0</timezone>
    </developer>
    <developer>
      <id>yperez</id>
      <name>Yasset Perez-Riverol</name>
      <email>ypriverol@gmail.com</email>
      <timezone>0</timezone>
    </developer>
  </developers>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <java.version>1.8</java.version>
    <uk.ac.ebi.jmzml-jmzml.version>1.7.11</uk.ac.ebi.jmzml-jmzml.version>
    <lombock.version>1.18.2</lombock.version>
    <slf4j.version>1.7.25</slf4j.version>
    <logback.version>1.2.3</logback.version>
    <avro.version>1.9.0</avro.version>
    <spark.version>2.4.3</spark.version>
    <scala.version>2.12.0</scala.version>
    <org.zeroturnaround.version>1.13</org.zeroturnaround.version>
    <ehcache.version>3.8.1</ehcache.version>
    <zoodb.version>0.5.2</zoodb.version>
    <chroniclemap.version>3.17.1</chroniclemap.version>
    <leveldb.version>0.10</leveldb.version>
    <junit.version>4.13.1</junit.version>
    <mockito-core.version>1.10.19</mockito-core.version>
    <hamcrest.version>1.3</hamcrest.version>
    <jackson.version>2.11.1</jackson.version>
  </properties>

  <dependencies>
    <dependency>
      <groupId>uk.ac.ebi.jmzml</groupId>
      <artifactId>jmzml</artifactId>
      <version>${uk.ac.ebi.jmzml-jmzml.version}</version>
    </dependency>

    <dependency>
      <groupId>io.github.bigbio.pgatk</groupId>
      <artifactId>pgatk-utilities</artifactId>
      <version>1.0.1-SNAPSHOT</version>
    </dependency>

    <dependency>
      <groupId>org.apache.avro</groupId>
      <artifactId>avro</artifactId>
      <version>1.11.3</version>
    </dependency>

    <dependency>
      <groupId>org.zeroturnaround</groupId>
      <artifactId>zt-zip</artifactId>
      <version>${org.zeroturnaround.version}</version>
      <type>jar</type>
    </dependency>

    <dependency>
      <groupId>org.projectlombok</groupId>
      <artifactId>lombok</artifactId>
      <version>${lombock.version}</version>
    </dependency>

    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>slf4j-api</artifactId>
      <version>${slf4j.version}</version>
    </dependency>
    <dependency>
      <groupId>org.slf4j</groupId>
      <artifactId>jcl-over-slf4j</artifactId>
      <version>${slf4j.version}</version>
    </dependency>


    <!-- In memory property storage -->
    <dependency>
      <groupId>net.openhft</groupId>
      <artifactId>chronicle-map</artifactId>
      <version>${chroniclemap.version}</version>
    </dependency>

    <!-- https://mvnrepository.com/artifact/org.iq80.leveldb/leveldb -->
    <dependency>
      <groupId>org.iq80.leveldb</groupId>
      <artifactId>leveldb</artifactId>
      <version>${leveldb.version}</version>
    </dependency>

    <dependency>
      <groupId>org.mapdb</groupId>
      <artifactId>mapdb</artifactId>
      <version>3.0.8</version>
    </dependency>

    <dependency>
      <groupId>com.spotify.sparkey</groupId>
      <artifactId>sparkey</artifactId>
      <version>3.0.1</version>
    </dependency>

    <dependency>
      <groupId>org.ehcache</groupId>
      <artifactId>ehcache</artifactId>
      <version>${ehcache.version}</version>
    </dependency>

    <dependency>
      <groupId>org.zoodb</groupId>
      <artifactId>zoodb</artifactId>
      <version>${zoodb.version}</version>
    </dependency>

    <!-- junit dependencies -->
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>${junit.version}</version>
    </dependency>
    <dependency>
      <groupId>org.hamcrest</groupId>
      <artifactId>hamcrest-library</artifactId>
      <version>${hamcrest.version}</version>
    </dependency>
    <dependency>
      <groupId>org.hamcrest</groupId>
      <artifactId>hamcrest-core</artifactId>
      <version>${hamcrest.version}</version>
    </dependency>
    <dependency>
      <groupId>org.mockito</groupId>
      <artifactId>mockito-core</artifactId>
      <version>${mockito-core.version}</version>
    </dependency>

    <!-- Dependecies for jaxb-->
    <dependency>
      <groupId>com.sun.xml.bind</groupId>
      <artifactId>jaxb-impl</artifactId>
      <version>2.3.2</version>
    </dependency>

    <dependency>
      <groupId>com.sun.xml.bind</groupId>
      <artifactId>jaxb-core</artifactId>
      <version>2.3.0.1</version>
    </dependency>

    <dependency>
      <groupId>com.fasterxml.jackson.core</groupId>
      <artifactId>jackson-core</artifactId>
      <version>${jackson.version}</version>
    </dependency>
    <dependency>
      <groupId>com.fasterxml.jackson.core</groupId>
      <artifactId>jackson-annotations</artifactId>
      <version>${jackson.version}</version>
    </dependency>
    <dependency>
      <groupId>com.fasterxml.jackson.core</groupId>
      <artifactId>jackson-databind</artifactId>
      <version>${jackson.version}</version>
    </dependency>
    <dependency>
      <groupId>com.fasterxml.jackson.module</groupId>
      <artifactId>jackson-module-paranamer</artifactId>
      <version>${jackson.version}</version>
    </dependency>

  </dependencies>

  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>true</filtering>
      </resource>
    </resources>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-release-plugin</artifactId>
        <version>2.5.3</version>
        <configuration>
          <remoteTagging>true</remoteTagging>
          <goals>deploy</goals>
        </configuration>
      </plugin>

    </plugins>
    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.5.1</version>
          <configuration>
            <source>${java.version}</source>
            <target>${java.version}</target>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-source-plugin</artifactId>
          <version>3.0.0</version>
          <executions>
            <execution>
              <id>attach-source</id>
              <goals>
                <goal>jar</goal>
              </goals>
            </execution>
          </executions>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <version>3.1.1</version>
          <executions>
            <execution>
              <id>generate-javadocs</id>
              <phase>generate-sources</phase>
              <goals>
                <goal>javadoc</goal>
              </goals>
              <configuration>
                <doclint>all,-missing</doclint>
                <reportOutputDirectory>${basedir}/docs</reportOutputDirectory>
                <doclint>none</doclint>
              </configuration>
            </execution>
            <execution>
              <id>attach-javadocs</id>
              <goals>
                <goal>jar</goal>
              </goals>
              <!-- Prevent that nasty error from Java 8 DocLint new feature -->
              <configuration>
                <doclint>all,-missing</doclint>
              </configuration>
            </execution>
          </executions>

        </plugin>
      </plugins>
    </pluginManagement>
  </build>

  <repositories>
    <repository>
      <id>nexus-ebi-release-repo</id>
      <url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
    </repository>
    <repository>
      <id>nexus-ebi-snapshot-repo</id>
      <url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/</url>
    </repository>
    <repository>
      <id>sonatype-release</id>
      <url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url>
    </repository>
    <repository>
      <id>sonatype-snapshopt</id>
      <url>https://oss.sonatype.org/content/repositories/snapshots</url>
    </repository>
    <repository>
      <!-- This repo is required for cpdetector (required by jmzidml->pride-xml-handler->xxindex->cpdetector) and related libraries -->
      <!-- This is supplied here because of an HTTP 301 Permanent Redirect on the old URL that xxindex supplies,
      which breaks fresh builds. -->
      <id>sammoa-group</id>
      <url>https://nexus.nuiton.org/nexus/content/groups/sammoa-group/</url>
    </repository>
  </repositories>

  <distributionManagement>
    <repository>
      <id>sonatype-release</id>
      <name>Central Repository OSSRH</name>
      <url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url>
    </repository>
    <snapshotRepository>
      <id>sonatype-snapshopt</id>
      <name>Central Repository OSSRH</name>
      <url>https://oss.sonatype.org/content/repositories/snapshots</url>
    </snapshotRepository>
  </distributionManagement>

  <scm>
    <connection>scm:git:https://github.com/bigbio/pgatk-io.git</connection>
    <developerConnection>scm:git:https://github.com/bigbio/pgatk-io.git</developerConnection>
    <url>https://github.com/bigbio/pgatk-io.git</url>
    <tag>HEAD</tag>
  </scm>

</project>