annotate tool_dependencies.xml @ 1:ab12adaa5cc2 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="biopython" version="1.61">
        <repository changeset_revision="5d0c54f7fea2" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <set_environment version="1.0">
        <environment_variable action="set_to" name="GLIMMER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <package name="glimmer" version="3.02b">
        <install version="1.0">
            <actions>
                <action type="download_file">http://www.cbcb.umd.edu/software/glimmer/glimmer302b.tar.gz</action>
                <action type="shell_command">tar xfvz glimmer302b.tar.gz</action>
                <action type="shell_command">cd ./glimmer3.02/src &amp;&amp; make</action>

                <action type="move_directory_files">
                    <source_directory>./glimmer3.02/bin</source_directory>
                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>To compile glimmer you need a C compiler (usually gcc).
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
http://www.cbcb.umd.edu/software/glimmer/</readme>
    </package>
</tool_dependency>