# HG changeset patch
# User jjohnson
# Date 1374758880 14400
# Node ID 378fc267bd0e62c223de4430d0809791c2de3f32

Uploaded

diff -r 000000000000 -r 378fc267bd0e tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 25 09:28:00 2013 -0400
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="velvet" version="1.2.10">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone git://github.com/dzerbino/velvet.git velvet</action>
+                <action type="shell_command">git reset --hard 5cea317b4ec5c3f0fd2931321bc7231d8a250682</action>
+                <action type="shell_command">make -i CATEGORIES=4 MAXKMERLENGTH=191 OPENMP=1</action>
+                <action type="shell_command">mkdir scripts</action>
+                <action type="shell_command">find contrib/[a-z]* -type f -name '*.p?' -exec cp -p {} scripts ";"</action>
+                <action type="shell_command">cp -rp contrib/VelvetOptimiser*/VelvetOpt* scripts</action>
+                <action type="shell_command">ls scripts</action>
+                <action type="move_file">
+                    <source>velvetg</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>velveth</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>scripts</source_directory>
+                    <destination_directory>$INSTALL_DIR/scripts</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="MAXKMERLENGTH" action="set_to">191</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="CATEGORIES" action="set_to">4</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Velvet is a sequence assembler for very short reads.
+            http://www.ebi.ac.uk/~zerbino/velvet/
+            This installs the velvet assembler version 1.2.10 and contributed scripts including VelvetOptimiser.pl 
+        </readme>
+    </package>
+</tool_dependency>