Mercurial > repos > fubar > differential_count_models

annotate tool_dependencies.xml @ 32:8051d14cf819 draft

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update with better filtering
author fubar
date Sun, 22 Dec 2013 01:32:29 -0500
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="package_r3" version="3.0.1">
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4 <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
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5 </package>
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6 <package name="biocbasics" version="2.12">
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7 <install version="1.0">
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8 <actions>
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9 <action type="set_environment_for_install">
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10 <repository changeset_revision="6344ee60d0cf" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
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11 <package name="r3" version="3.0.1" />
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12 </repository>
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13 </action>
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14 <action type="make_directory">$INSTALL_DIR</action>
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15 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
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16 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DEXSeq','ggplot2','gplots')" &gt;&gt; $INSTALL_DIR/runme.R</action>
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17 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
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18 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
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19 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
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20 <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp;
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21 R CMD BATCH $INSTALL_DIR/runme.R &gt; $INSTALL_DIR/install.log </action>
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22 <action type="shell_command">cat $INSTALL_DIR/install.log</action>
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23 </actions>
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24 </install>
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25 <readme>Installs some basic bioc packages for the edgeR wrapper
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26 It's clunky but this is the only way I could get anything installed into the package_r3 R
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27 </readme>
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28 </package>
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29 </tool_dependency>