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Fix SnpSift dependency
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 16:06:58 -0500
parents ef4598ea7179
children 24c77a318a0f
line wrap: on
line source

<?xml version="1.0"?>
<tool_dependency>
    <package name="snpEff" version="3.0">
        <install version="1.0">
            <actions>
                <action type="shell_command">wget http://sourceforge.net/projects/snpeff/files/snpEff_v3_0_core.zip; unzip snpEff_v3_0_core.zip; mv snpEff_3_0 snpEff</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>

                <action type="set_environment">
                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/snpEff</environment_variable>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/snpEff/scripts</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>
    <package name="SnpSift" version="1.7">
        <install version="1.0">
            <actions>
                <action type="shell_command">mkdir -p SnpSift; cd SnpSift; wget http://sourceforge.net/projects/snpeff/files/SnpSift_v1_7.jar</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="JAVA_JAR_PATH" action="prepend_to">$INSTALL_DIR/SnpSift</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>

</tool_dependency>