Mercurial > repos > bgruening > bismark

changeset 6:1c97427d28a3 draft

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Uploaded
author bgruening
date Thu, 18 Oct 2012 04:00:21 -0400
parents 045c0592c180
children 63d9e369c669
files bismark_wrapper/bismark_methylation_extractor.xml bismark_wrapper/bismark_wrapper.xml bismark_wrapper/tool_data_table_conf.xml.sample bismark_wrapper/tool_dependencies.xml
diffstat 4 files changed, 11 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- 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
 
--- 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">
--- 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="#">
--- 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>