view tool_dependencies.xml @ 4:496b2ca7ddb5 draft

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<?xml version="1.0"?>
<tool_dependency>
    <!--<set_environment version="1.0">
        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>-->
    <package name="macs2" version="2.0.10.2">
        <install version="1.0">           
            <actions>
                <action type="download_by_url">http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tar.bz2</action>
                <action type="shell_command">`pwd` > ~/test.out</action>
                <action type="shell_command">cd Python-2.7.3</action>
                <action type="shell_command">./configure</action>
                <action type="shell_command">make -j</action>
                <action type="shell_command">sudo make install</action>
                <action type="shell_command">sudo chmod ag+w /usr/local/lib/python2.7/site-packages</action>
                <action type="shell_command">sudo chmod ag+wx /usr/local/bin</action>
            </actions>
            <actions>
                <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/toolshed/dependencies/macs2/macs2pkg.tar?raw=true</action>
                <action type="move_directory_files">
                    <source_directory>bin</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>lib</source_directory>
                    <destination_directory>$INSTALL_DIR/lib</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Macs2 depends on having python2.7 installed on all nodes of the work cluster</readme>
    </package>
</tool_dependency>