# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1346986111 18000
# Node ID 12447208b8cba1f9282d58af689708486a3e5c1f
# Parent  13900a1ad862b10faf4958bde6cf7abc528ff4ac
Add tool_dependencies

diff -r 13900a1ad862 -r 12447208b8cb cd_hit_est.xml
--- a/cd_hit_est.xml	Thu Sep 06 22:28:46 2012 -0400
+++ b/cd_hit_est.xml	Thu Sep 06 21:48:31 2012 -0500
@@ -1,7 +1,7 @@
 <tool id="cd_hit_est" name="CD-HIT-EST" version="1.0">
  <description>Cluster a nucleotide dataset into representative sequences</description>
  <requirements>
-  <requirement type="package">cd-hit-est</requirement>
+  <requirement type="package" version="4.6.1">cd-hit-est</requirement>
  </requirements>
  <command>
   cd-hit-est -i $fasta_in -o rep_seq -c $similarity -n $wordsize $strand
diff -r 13900a1ad862 -r 12447208b8cb tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 06 21:48:31 2012 -0500
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="cd-hit" version="4.6.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz</action>
+                <action type="shell_command">make openmp=yes</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+These links provide information for building the cdhit package:
+
+http://weizhong-lab.ucsd.edu/cd-hit/
+
+https://code.google.com/p/cdhit/
+
+https://code.google.com/p/cdhit/source/browse/README
+
+        </readme>
+    </package>
+</tool_dependency>
+