# HG changeset patch
# User geert-vandeweyer
# Date 1406541093 14400
# Node ID 1b008b4b05f364d5545b42bcdad8839afe903cae

Uploaded

diff -r 000000000000 -r 1b008b4b05f3 readme.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Mon Jul 28 05:51:33 2014 -0400
@@ -0,0 +1,16 @@
+Galaxy tool_dependency for NovoAlign
+====================================
+
+This tool_dependency is written by Geert Vandeweyer. NovoAlign is a product of Novocraft, and is available only for open non-profit use without license.  
+
+To obtain Novoalign, go to http://www.novocraft.com/main/page.php?id=968
+
+Download the approriate package, unpack the folder and edit the NOVOALIGN_PATH environment variable in the file:
+
+<tool_dependency_dir>/environment_settings/NOVOALIGN_PATH/geert-vandeweyer/package_novoalign/<hash_string>/env.sh
+
+to point to the folder where you have installed NovoAlign.
+
+To prepare the index files, use:  novoindex <index.file.naidx> <fasta file(s)>
+
+Finally, you need to set up the <path>/galaxy-dist/tool-data/<toolshed>/repos/geert-vandeweyer/package_novoalign/<hash>/novoalign.loc file for the correct path of your index files.
diff -r 000000000000 -r 1b008b4b05f3 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Jul 28 05:51:33 2014 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of all index files under genome directory -->
+    <table name="novoalign" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="novoalign.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 1b008b4b05f3 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jul 28 05:51:33 2014 -0400
@@ -0,0 +1,28 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool_dependency>
+<package name="novoalign" version='latest'>
+	<install version='1.0'>
+		<actions>
+			<action type="set_environment">
+				<environment_variable action="set_to" name="NOVOALIGN_PATH">/Set/Path/to/NovoAlign/Installation/folder</environment_variable>	
+			</action>
+		</actions>
+	</install>
+	<readme>
+Galaxy tool_dependency for NovoAlign
+====================================
+
+This tool_dependency is written by Geert Vandeweyer. NovoAlign is a product of Novocraft, and is available only for open non-profit use without license.  
+
+To obtain Novoalign, go to http://www.novocraft.com/main/page.php?id=968
+
+Download the approriate package, unpack the folder and edit the NOVOALIGN_PATH environment variable in the file:
+
+&lt;tool_dependency_dir&gt;/environment_settings/NOVOALIGN_PATH/geert-vandeweyer/package_novoalign/&lt;hash_string&gt;/env.sh
+
+to point to the folder where you have installed NovoAlign.
+
+	</readme>
+</package>
+
+</tool_dependency>