<?xml version="1.0"?>
<tool_dependency>
  <package name="bowtie" version="0.12.7">
      <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="0.1.18">
      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="pysam" version="0.7.7">
      <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="R" version="3.0.3">
      <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="biocbasics" version="2.14">
      <install version="1.0">
          <actions>
              <action type="set_environment_for_install">
                  <repository changeset_revision="e509651776fa" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                      <package name="R" version="3.0.3" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR</action>
                <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action>
                <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
                <action type="shell_command">echo "installme=c(\"lattice\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
                <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
                <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
                <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
                <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
            </actions>
        </install>
    <package name="numpy" version="1.9">
        <repository name="package_numpy_1_9" owner="iuc" prior_installation_required="True" />
    </package>
    <package name="scipy" version="0.14">
        <repository name="package_scipy_0_14" owner="iuc" prior_installation_required="True" />
    </package>
        <readme>Installs some basic bioc packages for the lattice wrapper for managing lattice panels
        It's clunky but this is the most convenient way iuc could get anything installed into the package_r3
        Note we use cran at fred hutch since no fastest mirror thingy
       </readme>
    </package>
</tool_dependency>