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view tool_dependencies.xml @ 0:63ff807752d7 draft

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Imported from capsule None
author drosofff
date Mon, 03 Nov 2014 10:30:29 -0500
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children 6c72cf9a00df
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<?xml version="1.0"?>
<tool_dependency>
  <package name="bowtie" version="0.12.7">
      <repository changeset_revision="f54826948b0b" 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="240d1ad9f207" 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="9ff23e0b280b" 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="9ff23e0b280b" 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\",\"latticeExtra\")" &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 "install.packages(c(\"gridBase\",\"gridExtra\"),dependencies=T,repos=\"http://cran.us.r-project.org\")" &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>
        <readme>Installs some basic bioc packages for the lattice wrapper and grid + gridExtra 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>