Mercurial > repos > fubar > differential_count_models

comparison rgedgeR/tool_dependencies.xml @ 3:fe5c828dee80 draft

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Uploaded
author fubar
date Sat, 27 Jul 2013 00:25:33 -0400
parents df4fea3be1b3
children 78aa01cf762d
comparison
equal deleted inserted replaced
2:a612f61ff3b6 3:fe5c828dee80
20 <action type="make_directory">$INSTALL_DIR</action> 20 <action type="make_directory">$INSTALL_DIR</action>
21 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action> 21 <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &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> 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 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