pom.xml 6.09 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11
<!--

    Biopet is built on top of GATK Queue for building bioinformatic
    pipelines. It is mainly intended to support LUMC SHARK cluster which is running
    SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
    should also be able to execute Biopet tools and pipelines.

    Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center

    Contact us at: sasc@lumc.nl

12
    A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
13 14 15 16
    license; For commercial users or users who do not want to follow the AGPL
    license, please contact us to obtain a separate license.

-->
17 18 19 20
<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>

21
    <artifactId>BiopetPackage</artifactId>
22 23
    <packaging>jar</packaging>
    
24 25 26
    <parent>
        <groupId>nl.lumc.sasc</groupId>
        <artifactId>Biopet</artifactId>
27
        <version>0.9.0-SNAPSHOT</version>
28 29 30
        <relativePath>../</relativePath>
    </parent>
    
31
    <inceptionYear>2014</inceptionYear>
Peter van 't Hof's avatar
Peter van 't Hof committed
32
    <name>BiopetPackage</name>
33 34 35 36
    <url>http://maven.apache.org</url>

    <properties>
        <sting.shade.phase>package</sting.shade.phase>
37
        <app.main.class>nl.lumc.sasc.biopet.BiopetExecutableMain</app.main.class>
38 39 40 41 42
    </properties>

    <dependencies>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
43
            <artifactId>BiopetCore</artifactId>
44
            <version>${project.version}</version>
45
        </dependency>
46 47 48 49 50
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>GenerateIndexes</artifactId>
            <version>${project.version}</version>
        </dependency>
Peter van 't Hof's avatar
Peter van 't Hof committed
51 52 53
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Flexiprep</artifactId>
54
            <version>${project.version}</version>
Peter van 't Hof's avatar
Peter van 't Hof committed
55 56 57 58
        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Mapping</artifactId>
59
            <version>${project.version}</version>
Peter van 't Hof's avatar
Peter van 't Hof committed
60 61 62 63
        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>BamMetrics</artifactId>
64
            <version>${project.version}</version>
Peter van 't Hof's avatar
Peter van 't Hof committed
65 66 67 68
        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Gentrap</artifactId>
69
            <version>${project.version}</version>
Peter van 't Hof's avatar
Peter van 't Hof committed
70
        </dependency>
Peter van 't Hof's avatar
Peter van 't Hof committed
71 72 73 74 75
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>TinyCap</artifactId>
            <version>${project.version}</version>
        </dependency>
Peter van 't Hof's avatar
Peter van 't Hof committed
76 77 78
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Sage</artifactId>
79
            <version>${project.version}</version>
Peter van 't Hof's avatar
Peter van 't Hof committed
80 81 82
        </dependency>
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
83
            <artifactId>Kopisu</artifactId>
84
            <version>${project.version}</version>
Peter van 't Hof's avatar
Peter van 't Hof committed
85
        </dependency>
Wai Yi Leung's avatar
Wai Yi Leung committed
86 87
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
88
            <artifactId>GwasTest</artifactId>
Wai Yi Leung's avatar
Wai Yi Leung committed
89 90
            <version>${project.version}</version>
        </dependency>
91 92 93 94 95
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Gears</artifactId>
            <version>${project.version}</version>
        </dependency>
96 97
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
Peter van 't Hof's avatar
Peter van 't Hof committed
98
            <artifactId>Bam2Wig</artifactId>
99 100
            <version>${project.version}</version>
        </dependency>
101 102 103 104 105
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Carp</artifactId>
            <version>${project.version}</version>
        </dependency>
Sander Bollen's avatar
Sander Bollen committed
106 107 108 109 110
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Toucan</artifactId>
            <version>${project.version}</version>
        </dependency>
Peter van 't Hof's avatar
Peter van 't Hof committed
111 112 113 114 115
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Shiva</artifactId>
            <version>${project.version}</version>
        </dependency>
Peter van 't Hof's avatar
Peter van 't Hof committed
116 117 118 119 120
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Basty</artifactId>
            <version>${project.version}</version>
        </dependency>
121 122 123 124 125
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>BiopetToolsPackage</artifactId>
            <version>${project.version}</version>
        </dependency>
126 127 128 129 130 131
    </dependencies>
    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
132
                <version>2.4.1</version>
133
                <configuration>
Peter van 't Hof's avatar
Peter van 't Hof committed
134
                    <!--suppress MavenModelInspection -->
135 136 137 138 139
                    <finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                            <manifestEntries>
                                <Main-Class>${app.main.class}</Main-Class>
Peter van 't Hof's avatar
Peter van 't Hof committed
140
                                <!--suppress MavenModelInspection -->
141
                                <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
Peter van 't Hof's avatar
Peter van 't Hof committed
142
                                <!--suppress MavenModelInspection -->
143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161
                                <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
                            </manifestEntries>
                        </transformer>
                    </transformers>
                    <filters>
                    </filters>
                </configuration>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
</project>