annotate tool_dependencies.xml @ 2:85a4d7be4f65 draft default tip

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<?xml version="1.0"?>
<tool_dependency>
    <package name="mgescan" version="3.0.0">
        <install version="1.0">
            <actions_group>
            	<!--
                <actions architecture="x86_64" os="linux">
			<action type="download_by_url">
				https://github.com/MGEScan/mgescan/archive/1.1.tar.gz
			</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                -->
                <actions>
		<action type="download_by_url">
				https://github.com/MGEScan/mgescan/archive/1.1.tar.gz
                    </action>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" toolshed="https://toolshed.g2.bx.psu.edu">
                            <package name="trf" version="4.0" />
                        </repository>
                    </action>
                    <action type="shell_command">python setup.py install</action>
                    <action type="move_file">
                        <source>mgescan</source>
                        <destination>$INSTALL_DIR/mgescan</destination>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/mgescan</environment_variable>
                    <environment_variable action="set_to" name="MGESCAN_HOME">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="MGESCAN_SRC">$INSTALL_DIR/mgescan</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
Program: mgescan (Tools for identifying LTR &amp; nonLTR)
Version: 3.0 

Usage:
    mgescan both &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
    mgescan ltr &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
    mgescan nonltr &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
    mgescan (-h | --help)
    mgescan --version

        </readme>
    </package>
</tool_dependency>