# HG changeset patch
# User mzytnicki
# Date 1366799085 14400
# Node ID c181ca34432253ce5da2377d4ef7d1f2b2cdde3f
# Parent  1409d4dbf17eb4b1a915caae1cb336a26bc8ce1f
Uploaded

diff -r 1409d4dbf17e -r c181ca344322 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 24 06:23:03 2013 -0400
+++ b/tool_dependencies.xml	Wed Apr 24 06:24:45 2013 -0400
@@ -6,20 +6,8 @@
     <package name="samtools" version="0.1.12">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/tool_shed_dependencies/bamedit/samtoolspkg.tar</action>
-                <action type="shell_command">chmod ago+x samtools</action>
-                <action type="shell_command">chmod ago+x maq2sam-long</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
+				<action type="shell_command">R --slave --no-save --no-restore --quiet -e 'if (!require("RColorBrewer")){install.packages("RColorBrewer", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'</action>
+				<action type="shell_command">R --slave --no-save --no-restore --quiet -e 'if (!require("Hmisc")){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'</action>
             </actions>
         </install>
         <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>