view tool_dependencies.xml @ 108:96ebf676f6c0 draft

consolidated from baker version. includes anscombe robust fit option. Heatmap is wrong still and the r packages won't export with all their dependencies so testing is painful

<?xml version="1.0"?>
<tool_dependency>
    <package name="ghostscript" version="9.10">
        <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://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="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="r303" 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="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>