Mercurial > repos > fubar > differential_count_models

comparison tool_dependencies.xml @ 69:919822102c86 draft

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Uploaded
author fubar
date Mon, 17 Feb 2014 18:46:46 -0500
parents a2016dfb1de5
children e4291e5a03c1
comparison
equal deleted inserted replaced
68:a2016dfb1de5 69:919822102c86
22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action> 22 <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
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; $INSTALL_DIR/runme.R</action>
27 <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action> 27 <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>
28 </actions> 28 </actions>
29 </install> 29 </install>
30 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs 30 <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
31 It's clunky but this is the most convenient way I could get anything installed into the package_r3 31 It's clunky but this is the most convenient way I could get anything installed into the package_r3
32 Note we use cran at fred hutch since no fastest mirror thingy 32 Note we use cran at fred hutch since no fastest mirror thingy