pom.xml 7.29 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>0.10.0-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>
Sander Bollen's avatar
Sander Bollen committed
121 122 123 124 125
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>Tarmac</artifactId>
            <version>${project.version}</version>
        </dependency>
126 127 128 129 130
        <dependency>
            <groupId>nl.lumc.sasc</groupId>
            <artifactId>BiopetToolsPackage</artifactId>
            <version>${project.version}</version>
        </dependency>
131 132 133 134 135 136
    </dependencies>
    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
137
                <version>2.4.1</version>
138
                <configuration>
Peter van 't Hof's avatar
Peter van 't Hof committed
139 140
                    <shadedArtifactAttached>true</shadedArtifactAttached>
                    <shadedClassifierName>allinone</shadedClassifierName>
Peter van 't Hof's avatar
Peter van 't Hof committed
141
                    <!--suppress MavenModelInspection -->
142 143 144 145 146
                    <finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
                    <transformers>
                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                            <manifestEntries>
                                <Main-Class>${app.main.class}</Main-Class>
Peter van 't Hof's avatar
Peter van 't Hof committed
147
                                <!--suppress MavenModelInspection -->
148
                                <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
Peter van 't Hof's avatar
Peter van 't Hof committed
149
                                <!--suppress MavenModelInspection -->
150 151 152
                                <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
                            </manifestEntries>
                        </transformer>
Peter van 't Hof's avatar
Peter van 't Hof committed
153 154 155
                        <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                            <resource>reference.conf</resource>
                        </transformer>
156 157
                    </transformers>
                    <filters>
158 159 160 161 162 163 164 165
                        <filter>
                            <artifact>*:*</artifact>
                            <excludes>
                                <exclude>META-INF/*.SF</exclude>
                                <exclude>META-INF/*.DSA</exclude>
                                <exclude>META-INF/*.RSA</exclude>
                            </excludes>
                        </filter>
Peter van 't Hof's avatar
WIP  
Peter van 't Hof committed
166 167 168 169 170 171
                        <filter>
                            <artifact>javax.servlet:servlet-api:2.5</artifact>
                            <excludes>
                                <exclude>*.*</exclude>
                            </excludes>
                        </filter>
172 173 174 175 176 177 178 179 180 181 182 183 184 185
                    </filters>
                </configuration>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
</project>