annotate tool_dependencies.xml @ 0:0a21f73e2f15 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_transtermhp_2_09 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="transtermhp" version="2.09">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://transterm.cbcb.umd.edu/transterm_hp_v2.09.zip</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>transterm</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>2ndscore</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>calibrate.sh</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>make_expterm.py</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>mfold_rna.sh</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>expterm.dat</source>
                    <destination>$INSTALL_DIR/data</destination>
                </action>
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
                  <environment_variable action="set_to" name="TRANSTERM_EXPTERM_DAT">$INSTALL_DIR/data/expterm.dat</environment_variable>
                  <environment_variable action="set_to" name="TRANSTERMHP_ROOT_PATH">$INSTALL_DIR/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
TransTermHP v. 2.0 is a complete rewrite by Carl Kingsford of TransTerm v. 1.0,
originally written by Maria D. Ermolaeva. The first TransTermHP was described in
the paper:

 [1] Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and
     Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial
     Genomes. J Mol Biol 301, (1), 27-33 (2000)

TransTermHP v 2.0 is free software and is distributed under the GNU Public
License. See the file LICENSE.txt included with TransTermHP for complete
details.

This package ships with the built-in experm.dat file which ships with
transterm. In tools, this may be used as::

    transterm -p \$TRANSTERM_EXPTERM_DAT

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