<?xml version="1.0"?>
<tool_dependency>
  <package name="edge-pro" version="1.3.1">
    <install version="1.0">
      <actions>
        <action type="download_by_url">http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz</action>
        <action type="shell_command">make</action>
        <action type="move_file">
          <source>count</source>
          <destination>$INSTALL_DIR/bin</destination>
        </action>
        <action type="move_file">
          <source>edge.pl</source>
          <destination>$INSTALL_DIR/bin</destination>
        </action>
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
Dependencies of EDGE-pro which needs to be installed separately:
- bowtie2 ( http://bowtie-bio.sourceforge.net/bowtie2/ ), in particular bowtie2, bowtie2-align and bowtie2-build need to be in the $PATH . These are usually already installed for Galaxy;
- Switch Perl core module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).
    </readme>
  </package>
</tool_dependency>