Mercurial > repos > fubar > differential_count_models

comparison tool_dependencies.xml @ 104:39f7ed5b2fc1 draft

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Uploaded
author fubar
date Sun, 02 Mar 2014 23:45:54 -0500
parents 83dc8bc30254
children
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103:83dc8bc30254 104:39f7ed5b2fc1
16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/"> 16 <repository changeset_revision="4c934f6b342e" name="package_r303" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
17 <package name="r303" version="3.0.3" /> 17 <package name="r303" version="3.0.3" />
18 </repository> 18 </repository>
19 </action> 19 </action>
20 <action type="make_directory">$INSTALL_DIR</action> 20 <action type="make_directory">$INSTALL_DIR</action>
21 <action type="shell_command">echo 'bioclite="http://bioconductor.org/biocLite.R"' &gt; $INSTALL_DIR/runme.R</action> 21 <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action>
22 <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action> 22 <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
23 <action type="shell_command">echo 'installme=c("edgeR","limma","DESeq","DESeq2")' &gt;&gt; $INSTALL_DIR/runme.R</action> 23 <action type="shell_command">echo "installme=c(\"edgeR\",\"limma\",\"DESeq\",\"DESeq2\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
24 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action> 24 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
25 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action> 25 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
26 <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> 26 <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>
27 <action type="shell_command">echo 'quit(save="no")' &gt;&gt; $INSTALL_DIR/runme.R</action> 27 <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
28 <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action> 28 <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action>
29 <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action> 29 <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action>
30 <action type="shell_command">export PATH=$PATH &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action> 30 <action type="shell_command">export PATH=$PATH &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>
31 </actions> 31 </actions>
32 </install> 32 </install>