# HG changeset patch
# User crs4
# Date 1421689731 18000
# Node ID ddcbf8732706e46e3774201dd61bfe76b21ea9fb
# Parent  bad8a51514ddbb3986eea0ba1bf51b73cf8caf60
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.

diff -r bad8a51514dd -r ddcbf8732706 COPYING
--- a/COPYING	Wed Mar 05 06:44:35 2014 -0500
+++ b/COPYING	Mon Jan 19 12:48:51 2015 -0500
@@ -1,7 +1,7 @@
-Copyright © 2012-2014 CRS4 Srl. http://www.crs4.it/
+Copyright © 2012-2015 CRS4 Srl. http://www.crs4.it/
 Created by:
 Paolo Uva <paolo.uva@crs4.it>
-Nicola Soranzo <nicola.soranzo@crs4.it>
+Nicola Soranzo <nicola.soranzo@tgac.ac.uk>
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the
diff -r bad8a51514dd -r ddcbf8732706 edge_pro.py
diff -r bad8a51514dd -r ddcbf8732706 edge_pro.xml
--- a/edge_pro.xml	Wed Mar 05 06:44:35 2014 -0500
+++ b/edge_pro.xml	Mon Jan 19 12:48:51 2015 -0500
@@ -112,19 +112,22 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: http://opensource.org/licenses/MIT
 
-If you use this tool in Galaxy, please cite |Cuccuru2013|_.
-
-.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
-.. _Cuccuru2013: http://orione.crs4.it/
-
-This tool uses `EDGE-pro`_, which is licensed separately. Please cite |Magoc2013|_.
+You can use this tool only if you agree to the license terms of: `EDGE-pro`_.
 
 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Magoc2013|_.
+
+.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
 .. |Magoc2013| replace:: Magoc, T., Wood, D., Salzberg, S. L. (2013) EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. *Evol. Bioinform.* 2013:9, 127-136
 .. _Magoc2013: http://www.la-press.com/edge-pro-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586
   </help>
diff -r bad8a51514dd -r ddcbf8732706 get_edge_data.xml
--- a/get_edge_data.xml	Wed Mar 05 06:44:35 2014 -0500
+++ b/get_edge_data.xml	Mon Jan 19 12:48:51 2015 -0500
@@ -25,14 +25,14 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
 
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _MIT license: http://opensource.org/licenses/MIT
 
-If you use this tool in Galaxy, please cite |Cuccuru2013|_.
+If you use this tool, please cite |Cuccuru2014|_.
 
-.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
-.. _Cuccuru2013: http://orione.crs4.it/
+.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
   </help>
 </tool>
diff -r bad8a51514dd -r ddcbf8732706 readme.rst
--- a/readme.rst	Wed Mar 05 06:44:35 2014 -0500
+++ b/readme.rst	Mon Jan 19 12:48:51 2015 -0500
@@ -26,6 +26,7 @@
 Version history
 ---------------
 
+- Release 3: Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
 - Release 2: Directly call edge.pl, remove edge_pro.py . Move minimun and maximum insert size params to paired library section. Update Orione citation.
 - Release 1: Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
 - Release 0: Initial release in the Tool Shed.
diff -r bad8a51514dd -r ddcbf8732706 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 05 06:44:35 2014 -0500
+++ b/tool_dependencies.xml	Mon Jan 19 12:48:51 2015 -0500
@@ -1,12 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="bowtie2" version="2.1.0">
-    <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="edge-pro" version="1.3.1">
     <install version="1.0">
       <actions>
         <action type="download_by_url">http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz</action>
+        <!-- Search executables in PATH instead of the CWD -->
+        <action type="shell_command">sed -i -e 's|$sourceDir/||' edge.pl</action>
         <action type="shell_command">make</action>
         <action type="move_file">
           <source>count</source>