Mercurial > repos > yhoogstrate > featurecounts

diff tool_dependencies.xml @ 6:fae19d64e9de draft

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Uploaded
author yhoogstrate
date Thu, 13 Nov 2014 09:46:22 -0500
parents 9fcffbe6c206
children 2312bedfe2a3
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed May 21 08:27:05 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 13 09:46:22 2014 -0500
@@ -6,30 +6,40 @@
 				<action type="shell_command">wget http://sourceforge.net/projects/subread/files/subread-1.4.4/subread-1.4.4-source.tar.gz &amp;&amp; tar -zxvf subread-1.4.4-source.tar.gz &amp;&amp; cd subread-1.4.4-source/src/ &amp;&amp; make -f Makefile.Linux &amp;&amp; cd ../../</action>
 				<action type="move_file">
 					<source>../subread-1.4.4-source/bin/featureCounts</source>
-					<destination>$INSTALL_DIR/bin</destination>
+					<destination>$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>
+					<!--<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>-->
 				</action>
 			</actions>
 		</install>
 		<readme>
-			Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed!
+			Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed.
 		</readme>
 	</package>
 	
 	<package name="featurecounts2bed" version="1.0.0">
 		<install version="1.0">
 			<actions>
+				<action type="move_file">
+					<source>$REPOSITORY_INSTALL_DIR/featurecounts2bed.sh</source>
+					<destination>$INSTALL_DIR/bin/</destination>
+				</action>
+				<!--
+				Revert to the previous if the move command doesn't work
+				
 				<action type="shell_command">wget http://testtoolshed.g2.bx.psu.edu/repos/yhoogstrate/featurecounts/raw-file/tip/featurecounts2bed.sh &amp;&amp; chmod 755 *.sh</action>
 				<action type="move_file">
 					<source>../featurecounts2bed.sh</source>
 					<destination>$INSTALL_DIR/bin</destination>
 				</action>
+				-->
+				<action type="chmod">
+					<file mode="555">$INSTALL_DIR/bin/featurecounts2bed.sh</file>
+				</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>