view tool_dependencies.xml @ 48:1c6c7e481be7 draft

removed atlas - won't compile here at the Baker - thinks we have cpu scaling turned on. We don't afaik.

<?xml version="1.0"?>
<tool_dependency>
<!--  
    this will not compile for me - it thinks we have autoscaling on
    - so we need libopenblas-base installed on all nodes...grrr
	<package name="atlas" version="3.11.11">
		<repository name='package_atlas_3_11' owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    and we need this added to the set_environment section below too
                    <repository name="package_atlas_3_11" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                        <package name="atlas" version="3.11.11" />
                    </repository>
-->
    <package name="r3" version="3.0.1">
        <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="ghostscript" version="9.07">
        <repository changeset_revision="7245d8573fca" name="package_ghostscript_9_07" owner="iuc" 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="biocbasics" version="2.12">
        <install version="1.0"> 
            <actions>
                <action type="set_environment_for_install">
                    <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" 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','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; $INSTALL_DIR/runme.R</action>                
                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </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
        copyright ross lazarus last updated december 2013 ross stop lazarus at gmail stop com
        License to use this source (dependencies have their own obligations) 
        is made available to you under the terms of the LGPL 
       </readme>
    </package>
</tool_dependency>