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view tool_dependencies.xml @ 6:e6b662b96061

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Fix typo in tool_dependencies.xml
author Jim Johnson <jj@umn.edu>
date Fri, 14 Sep 2012 13:57:58 -0500
parents ceaa79a5ee16
children 3cb1d19d57d1
line wrap: on
line source

<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
    </set_environment>
    <package name="snpEff" version="3.0f">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip/download</action>
                <action type="shell_command">pwd</action>
                <action type="shell_command">ls</action>
                <action type="move_file">
                    <source>SnpSift.jar</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>snpEff.jar</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>scripts</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="move_file">
                    <source>snpEff.config</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>

</tool_dependency>