Mercurial > repos > fubar > differential_count_models

comparison tool_dependencies.xml @ 109:86bd60bea4d8 draft

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Uploaded
author fubar
date Sun, 06 Jul 2014 20:37:19 -0400
parents 96ebf676f6c0
children d7e2a0c0cce9
comparison
equal deleted inserted replaced
108:96ebf676f6c0 109:86bd60bea4d8
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">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
29 <action type="shell_command">echo "R_PATH=$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>
31 </actions> 29 </actions>
32 </install> 30 </install>
33 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs 31 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
34 It's clunky but this is the most convenient way I could get anything installed into the package_r3 32 It's clunky but this is the most convenient way I could get anything installed into the package_r3
35 Note we use cran at fred hutch since no fastest mirror thingy 33 Note we use cran at fred hutch since no fastest mirror thingy