annotate tool_dependencies.xml @ 1:c4ad58c4bc7d draft

Add version_command element. Add test case from Joachim Jacob's blat wrapper: http://testtoolshed.g2.bx.psu.edu/view/joachim-jacob/blat . Add readme section to tool_dependencies.xml .

<?xml version="1.0"?>
<tool_dependency>
  <package name="blat" version="35">
<!--    <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type -->
    <install version="1.0">
      <actions>
        <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
        <action type="shell_command">export MACHTYPE=`uname -m` &amp;&amp; export HOME=$INSTALL_DIR &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make</action>
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/`uname -m`</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git

Please note that the BLAT source and executables are freely available for
academic, nonprofit and personal use. Commercial licensing information is
available on the Kent Informatics website (http://www.kentinformatics.com/).
    </readme>
  </package>
</tool_dependency>