# HG changeset patch
# User yhoogstrate
# Date 1384871676 18000
# Node ID becb1755e0960fcaa9b9919136ed1db07fa00cf9
# Parent  98c9492ef3367a2a86fe130b53f913c7ddbec79d
Uploaded

diff -r 98c9492ef336 -r becb1755e096 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Nov 19 09:30:40 2013 -0500
+++ b/tool_dependencies.xml	Tue Nov 19 09:34:36 2013 -0500
@@ -3,14 +3,19 @@
 	<package name="featurecounts_valid_gff" version="1.4.0.1">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">svn checkout https://featurecounts-valid-gff.googlecode.com/svn/trunk/ featurecounts-valid-gff &amp;&amp; cd featurecounts-valid-gff/src &amp;&amp; make -f Makefile.Linux &amp;&amp; cp ../bin/featureCounts ../../ 2> /dev/null ; cd ../bin ; ls ; cd .. ; echo "" ; echo "-----" ; echo "" ; ls -als ; cd .. ; echo "" ; echo "-----" ; echo "" ; ls -als ; echo "" ; whoami ; cp featureCounts bin/featurteCounts ; cp featureCounts $INSTALL_DIR/bin/featureCounts</action>
+				<action type="shell_command">svn checkout https://featurecounts-valid-gff.googlecode.com/svn/trunk/ featurecounts-valid-gff &amp;&amp; cd featurecounts-valid-gff/src &amp;&amp; make -f Makefile.Linux &amp;&amp; chmod 777 ../bin/* ; cp ../bin/featureCounts ../../ 2> /dev/null ; cd ../bin ; ls ; cd .. ; echo "" ; echo "-----" ; echo "" ; ls -als ; cd .. ; echo "" ; echo "-----" ; echo "" ; ls -als ; echo "" ; whoami ; cp featureCounts bin/featurteCounts ; cp featureCounts $INSTALL_DIR/bin/featureCounts</action>
 				<action type="move_file">
 					<source>featureCounts</source>
-					<destination>$INSTALL_DIR/bin/featureCounts</destination>
+					<destination>$INSTALL_DIR/bin</destination>
 				</action>
+				<action type="set_environment">
+					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+				</action>    
 			</actions>
 		</install>
 		<readme>
+			Downloads and installs featureCounts-valid-gff; requires SVN to be installed!
 		</readme>
 	</package>
 </tool_dependency>