# HG changeset patch
# User bgruening
# Date 1350547221 14400
# Node ID 1c97427d28a3cefeb4bd35a9f82d86a5e6c653fd
# Parent  045c0592c1805c61bf01a76303c2745c59bc2bc2
Uploaded

diff -r 045c0592c180 -r 1c97427d28a3 bismark_wrapper/bismark_methylation_extractor.xml
--- a/bismark_wrapper/bismark_methylation_extractor.xml	Sat Oct 13 02:58:26 2012 -0400
+++ b/bismark_wrapper/bismark_methylation_extractor.xml	Thu Oct 18 04:00:21 2012 -0400
@@ -2,9 +2,6 @@
     <!-- Wrapper compatible with Bismark version 0.7.7 -->
     <description>methylation extractor</description>
     <version_command>bismark_methylation_extractor --version</version_command>
-    <requirements>
-        <requirement type="package">bismark_methylation_extractor</requirement>
-    </requirements>
     <command interpreter="python">
         bismark_methylation_extractor.py
 
diff -r 045c0592c180 -r 1c97427d28a3 bismark_wrapper/bismark_wrapper.xml
--- a/bismark_wrapper/bismark_wrapper.xml	Sat Oct 13 02:58:26 2012 -0400
+++ b/bismark_wrapper/bismark_wrapper.xml	Thu Oct 18 04:00:21 2012 -0400
@@ -3,9 +3,8 @@
     <description>bisulfite mapper</description>
     <version_command>bismark --version</version_command>
     <requirements>
-        <requirement type="package">bismark</requirement>
-        <requirement type="package">bismark_genome_preparation</requirement>
         <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
+        <requirement type="package" version="0.7.7">bismark</requirement>
     </requirements>
     <parallelism method="basic"></parallelism>
     <command interpreter="python">
diff -r 045c0592c180 -r 1c97427d28a3 bismark_wrapper/tool_data_table_conf.xml.sample
--- a/bismark_wrapper/tool_data_table_conf.xml.sample	Sat Oct 13 02:58:26 2012 -0400
+++ b/bismark_wrapper/tool_data_table_conf.xml.sample	Thu Oct 18 04:00:21 2012 -0400
@@ -1,4 +1,3 @@
-<!-- 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 indexes in the Bismark mapper format -->
     <table name="bismark_indexes" comment_char="#">
diff -r 045c0592c180 -r 1c97427d28a3 bismark_wrapper/tool_dependencies.xml
--- a/bismark_wrapper/tool_dependencies.xml	Sat Oct 13 02:58:26 2012 -0400
+++ b/bismark_wrapper/tool_dependencies.xml	Thu Oct 18 04:00:21 2012 -0400
@@ -22,4 +22,14 @@
 Compiling bowtie2 requires zlib and libpthread to be present on your system.
         </readme>
     </package>
+    <package name="bismark" version="0.7.7">
+        <install version="1.0">
+            <set_environment version="1.0">
+                <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+            </set_environment>
+        </install>
+        <readme>
+bismark, bismark_genome_preparation and bismark_methylation_extractor are shipped with that wrapper
+        </readme>
+    </package>
 </tool_dependency>