Mercurial > repos > fubar > edger_test

<?xml version="1.0"?>
<tool_dependency>
    <!-- swap to bjorn gruening's much better R 3.0 package. Especially now that altas doesn't shrug on my laptop :) -->
    <package name="package_r_3_0_1" version="3.0.1">
        http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_r_3_0_1
        <repository changeset_revision="1d5580f2ece0" name="package_r_3_0_1" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="biocbasics" version="2.12">
        <install version="1.0">
            <actions>
                <action type="set_environment_for_install">
                    <repository changeset_revision="1d5580f2ece0" name="package_r_3_0_1" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="r3" version="3.0.1" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR</action>
                <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
                <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots')" &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; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp;
                 R CMD BATCH $INSTALL_DIR/runme.R &gt; $INSTALL_DIR/install.log </action>
                <action type="shell_command">cat $INSTALL_DIR/install.log</action>
             </actions>
        </install>
        <readme>Installs some basic bioc packages for the edgeR wrapper
        It's clunky but this is seems to install bioc things in package_r3 R
        There are more dependencies like xml2lib and curl - if not in buildessentials that probably belong in the R package installer
        Send code.
       </readme>
    </package>
</tool_dependency>
author	fubar
date	Mon, 08 Jul 2013 03:38:19 -0400
parents	1212dc390f4f
children