# HG changeset patch
# User yhoogstrate
# Date 1416409679 18000
# Node ID 2312bedfe2a35f23bba173149e54d3296a2c2166
# Parent  fae19d64e9de773f01c1c59adbc66133de8cc8b5
Uploaded

diff -r fae19d64e9de -r 2312bedfe2a3 README.md
--- a/README.md	Thu Nov 13 09:46:22 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-FeatureCounts wrapper for Galaxy
-================================
-
-<http://bioinf.wehi.edu.au/featureCounts/>
-<http://subread.sourceforge.net/>
-
-FeatureCounts as part of the SUBREAD package is "a highly efficient and
-accurate read summarization program".
-
-Development
------------
-
-* Repository-Maintainer: Youri Hoogstrate
-
-* Repository-Development: <https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools>
-
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus
-Medical Center (Rotterdam, Netherlands) on behalf of the Translational
-Research IT (TraIT) project:
-
-<http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch>
-
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
-
-<http://toolshed.dtls.nl/>
-
-License
--------
-
-**featureCounts**:
-
-GPL (>=3)
-
-**featurecounts2bed**:
-
-GPL (>=3)
-
-**This wrapper**:
-
-    Copyright (C) 2013-2014  Youri Hoogstrate
-
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
diff -r fae19d64e9de -r 2312bedfe2a3 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Nov 19 10:07:59 2014 -0500
@@ -0,0 +1,53 @@
+FeatureCounts wrapper for Galaxy
+================================
+
+http://bioinf.wehi.edu.au/featureCounts/
+http://subread.sourceforge.net/
+
+FeatureCounts as part of the SUBREAD package is "a highly efficient and
+accurate read summarization program".
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+
+* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+
+http://toolshed.dtls.nl/
+
+License
+-------
+
+**featureCounts**:
+
+GPL (>=3)
+
+**featurecounts2bed**:
+
+GPL (>=3)
+
+**This wrapper**:
+
+    Copyright (C) 2013-2014  Youri Hoogstrate
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
diff -r fae19d64e9de -r 2312bedfe2a3 featurecounts.xml
--- a/featurecounts.xml	Thu Nov 13 09:46:22 2014 -0500
+++ b/featurecounts.xml	Wed Nov 19 10:07:59 2014 -0500
@@ -236,7 +236,7 @@
 License
 -------
 
-featureCounts / subread package:
+**featureCounts / subread package**:
 
 - GNU General Public License version 3.0 (GPLv3)
 
@@ -246,12 +246,16 @@
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
 Research IT (TraIT) project:
+
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
 More tools by the Translational Research IT (TraIT) project can be found
 in the following toolsheds:
-- http://toolshed.dtls.nl/
-- http://toolshed.g2.bx.psu.edu
-- http://testtoolshed.g2.bx.psu.edu/
+
+http://toolshed.dtls.nl/
+
+http://toolshed.g2.bx.psu.edu/
+
+http://testtoolshed.g2.bx.psu.edu/
 </help>
 </tool>
diff -r fae19d64e9de -r 2312bedfe2a3 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 13 09:46:22 2014 -0500
+++ b/tool_dependencies.xml	Wed Nov 19 10:07:59 2014 -0500
@@ -22,24 +22,13 @@
 	<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="shell_command">mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/featurecounts2bed.sh $INSTALL_DIR/bin/</action>
 				<action type="chmod">
-					<file mode="555">$INSTALL_DIR/bin/featurecounts2bed.sh</file>
+					<file mode="755">$INSTALL_DIR/bin/featurecounts2bed.sh</file>
 				</action>
 				<action type="set_environment">
 					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
 				</action>
 			</actions>
 		</install>