Mercurial > repos > fubar > differential_count_models

diff 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
line wrap: on
line diff
--- a/tool_dependencies.xml	Sun Mar 02 23:26:35 2014 -0500
+++ b/tool_dependencies.xml	Sun Mar 02 23:45:54 2014 -0500
@@ -18,13 +18,13 @@
                     </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR</action>
-                <action type="shell_command">echo 'bioclite="http://bioconductor.org/biocLite.R"' &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "bioclite=\"http://bioconductor.org/biocLite.R\"" &gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "source(bioclite)" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo 'installme=c("edgeR","limma","DESeq","DESeq2")' &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "installme=c(\"edgeR\",\"limma\",\"DESeq\",\"DESeq2\")" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
                 <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <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>
-                <action type="shell_command">echo 'quit(save="no")' &gt;&gt; $INSTALL_DIR/runme.R</action>                
+                <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>
+                <action type="shell_command">echo "quit(save=\"no\")" &gt;&gt; $INSTALL_DIR/runme.R</action>                
                 <action type="shell_command">echo "PATH=$PATH 1&gt;&amp;2"</action>                
                 <action type="shell_command">echo "R_PATH=$R_PATH 1&gt;&amp;2"</action>                
                 <action type="shell_command">export PATH=$PATH &amp;&amp; $R_PATH/R CMD BATCH $INSTALL_DIR/runme.R </action>