<?xml version="1.0"?>
<tool_dependency>
  <package name="bowtie2" version="2.1.0">
    <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <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 action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
Dependencies of EDGE-pro which needs to be installed separately:
- Switch Perl module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).

Configuration: Previously (until Release 0), the EDGE_PRO_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use (--num-threads). This is not used anymore and may be removed.
    </readme>
  </package>
</tool_dependency>