view tool_dependencies.xml @ 102:851f3946c9d9 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="ghostscript" version="9.07">
        <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="graphicsmagick" version="1.3.18">
        <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="r303" version="3.0.3">
        <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" prior_installation_required="True" toolshed="http://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="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="r303" 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("edgeR","limma","DESeq","DESeq2")' &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("stringr","gplots"),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; $INSTALL_DIR/runme.R</action>                
                <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action>                
                <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action>                
                <action type="shell_command">export PATH=$PATH &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>
            </actions>
        </install>
        <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
        It's clunky but this is the most convenient way I could get anything installed into the package_r3
        Note we use cran at fred hutch since no fastest mirror thingy
        If atlas will not compile - eg: it thinks autoscaling is on or something,
        you need (eg for ubuntu) libopenblas-base installed on all nodes after commenting or removing all atlas references
       </readme>
    </package>
</tool_dependency>