# HG changeset patch
# User bgruening
# Date 1350029843 14400
# Node ID 5226800b84caccfe29a432e73a80e4f3a5c63ccd
# Parent  39ac0c2600ea9d358c5baf1e63cd61c28236233f
Uploaded

diff -r 39ac0c2600ea -r 5226800b84ca bismark_wrapper/bismark_wrapper.xml
--- a/bismark_wrapper/bismark_wrapper.xml	Fri Oct 12 04:08:03 2012 -0400
+++ b/bismark_wrapper/bismark_wrapper.xml	Fri Oct 12 04:17:23 2012 -0400
@@ -1,6 +1,6 @@
 <tool id="bismark" name="Bismark" version="0.7.7.1">
     <!-- Wrapper compatible with Bismark version 0.7.7 -->
-    <description>is a bisulfite mapper</description>
+    <description>bisulfite mapper</description>
     <version_command>bismark --version</version_command>
     <requirements>
         <requirement type="package">bismark</requirement>
diff -r 39ac0c2600ea -r 5226800b84ca bismark_wrapper/tool_dependencies.xml
--- a/bismark_wrapper/tool_dependencies.xml	Fri Oct 12 04:08:03 2012 -0400
+++ b/bismark_wrapper/tool_dependencies.xml	Fri Oct 12 04:17:23 2012 -0400
@@ -23,4 +23,13 @@
 Compiling bowtie2 requires zlib and libpthread to be present on your system.
         </readme>
     </package>
+    <!-- We ship bismark with that wrapper, so we only need to set the PATH variable -->
+    <package name="bismark">
+        <install version="1.0">
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">./</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
 </tool_dependency>