# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1386254391 21600
# Node ID 7d060ea51c6ffdba9823a625ac723f37788e63d5
# Parent  9fa1826ae6d4242c219e09b124ec7ec8ec164a6b
RSEM needs samtools in relative path to install

diff -r 9fa1826ae6d4 -r 7d060ea51c6f tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 11 13:11:36 2013 -0500
+++ b/tool_dependencies.xml	Thu Dec 05 08:39:51 2013 -0600
@@ -5,7 +5,11 @@
             <actions>
                 <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz</action>
                 <action type="shell_command">make</action>
-
+                <action type="make_directory">$INSTALL_DIR/bin/sam</action> 
+                <action type="move_file">
+                    <source>sam/samtools</source>
+                    <destination>$INSTALL_DIR/bin/sam</destination>
+                </action>
                 <action type="move_file">
                     <source>convert-sam-for-rsem</source>
                     <destination>$INSTALL_DIR/bin</destination>