Mercurial > repos > fubar > differential_count_models

comparison tool_dependencies.xml @ 90:2c7b33c84904 draft

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Uploaded
author fubar
date Thu, 27 Feb 2014 05:29:51 -0500
parents 6b95cd9e2648
children 6fb919a3bff4
comparison
equal deleted inserted replaced
89:7de681a7c511 90:2c7b33c84904
23 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action> 23 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
24 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action> 24 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
25 <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> 25 <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 "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action> 26 <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>
27 <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action> 27 <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action>
28 <action type="shell_command">export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action> 28 <action type="shell_command">export PATH=$PATH &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
29 </actions> 29 </actions>
30 </install> 30 </install>
31 <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
32 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
33 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