annotate tool_dependencies.xml @ 3:536f7bb5616d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tophat_2_0_14 commit 93bd8341966e13b91bbcb2b9bce75f0c0e7e1d92

<?xml version="1.0"?>
<tool_dependency>
    <package name="tophat" version="2.0.14">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-2.0.14-Linux-x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="shell_command">sed -i.bak 's#/build/dest#$INSTALL_DIR#' $INSTALL_DIR/bin/tophat2</action>
                </actions>
                <actions>
                    <action type="download_by_url">http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz</action>
                    <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                    <action type="make_install" />
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme />
    </package>
</tool_dependency>