--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 17 09:41:18 2013 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="sspace" version="2.0">
+    <install version="1.0">
+      <actions>
+        <action type="download_by_url" target_filename="SSPACE-BASIC-2.0_linux-x86_64.zip">http://www.baseclear.com/download.php?file_id=1038</action>
+        <!-- fix for Perl >= 5.16.0-->
+        <action type="shell_command">sed -i -e 's/require "getopts.pl"/use Getopt::Std/' -e 's/&amp;Getopts/getopts/' SSPACE_Basic_v2.0.pl</action>
+        <action type="move_directory_files">
+          <source_directory>.</source_directory>
+          <destination_directory>$INSTALL_DIR</destination_directory>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+        </action>
+        <action type="set_environment">
+          <environment_variable name="SSPACE_SITE_OPTIONS" action="set_to">"-T 1"</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+Change the SSPACE_SITE_OPTIONS variable in the installed env.sh file to adjust the number of threads to use in Bowtie alignment (-T).
+    </readme>
+  </package>
+</tool_dependency>