# HG changeset patch
# User fubar
# Date 1393821954 18000
# Node ID 39f7ed5b2fc1acbbd2538c70a8a128ae6478633a
# Parent  83dc8bc3025429985b3eac6c5fd651000935ac2a
Uploaded

diff -r 83dc8bc30254 -r 39f7ed5b2fc1 tool_dependencies.xml
--- 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>