Mercurial > repos > fubar > edger_test

comparison rgedgeR/tool_dependencies.xml @ 49:c4f8c9a00c0e draft

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author fubar
date Fri, 26 Jul 2013 22:47:38 -0400
parents e622f665c61c
children
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48:91e77df18a7f 49:c4f8c9a00c0e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="package_r3" version="3.0.1"> 3 <package name="r3" version="3.0.1">
4 <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> 4 <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
5 </package> 5 </package>
6 <package name="biocbasics" version="2.12"> 6 <package name="biocbasics" version="2.12">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <action type="set_environment_for_install"> 9 <action type="set_environment_for_install">
10 <repository changeset_revision="6f249fadd4ec" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> 10 <repository changeset_revision="1ffaf8412079" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
11 <package name="r3" version="3.0.1" /> 11 <package name="r3" version="3.0.1" />
12 </repository> 12 </repository>
13 </action> 13 </action>
14 <action type="make_directory">$INSTALL_DIR</action> 14 <action type="make_directory">$INSTALL_DIR</action>
15 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action> 15 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
16 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2','gplots')" &gt;&gt; $INSTALL_DIR/runme.R</action> 16 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
17 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action> 17 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
18 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action> 18 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
19 <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T)" &gt;&gt; $INSTALL_DIR/runme.R</action>
19 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action> 20 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
20 <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action> 21 <action type="shell_command"> export PATH=$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>
21 </actions> 22 </actions>
22 </install> 23 </install>
23 <readme>Installs some basic bioc packages for the edgeR wrapper 24 <readme>Installs some basic bioc packages for the edgeR wrapper