# HG changeset patch
# User fubar
# Date 1380417482 14400
# Node ID 322df5780b1912b6d7565126316759477c4c2be5
# Parent  5022cd74093c384d34e00762d7b1ec68a3e7c5da
Uploaded

diff -r 5022cd74093c -r 322df5780b19 freebayes-d291dc763c4c/freebayes.xml
--- a/freebayes-d291dc763c4c/freebayes.xml	Sat Sep 28 06:48:44 2013 -0400
+++ b/freebayes-d291dc763c4c/freebayes.xml	Sat Sep 28 21:18:02 2013 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
-<tool id="freebayes" name="FreeBayes" version="0.9.9">
+<tool id="freebayes" name="FreeBayes" version="8e44a20fccfe6c5c63f7e8aeb0f53548bf2e2ba7">
   <stdio>
-   <regex match=".*" source="both" level="warning" description="freebayes said:"/>
+   <regex match=".*" source="both" level="warning" description="freebayes:"/>
   </stdio>
   <requirements>
-    <requirement type="package" version="0.9.9_c993c5c07e7673">freebayes</requirement>
+    <requirement type="package" version="8e44a20fccfe6c5c63f7e8aeb0f53548bf2e2ba7">freebayes</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <description> - Bayesian genetic variant detector</description>
@@ -442,7 +442,7 @@
 
 In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. 
 
-Go FreeBayesMarth_ for details on FreeBayes.
+See FreeBayesMarth_ for details
 
 or FreeBayesGit_ for source
 
@@ -681,8 +681,7 @@
 
 .. _FreeBayesMarth: http://bioinformatics.bc.edu/marthlab/FreeBayes
 
-.. _FreeBayesGit: https://github.com/ekg/freebayes
+.. _FreeBayesGit: http://github.com/ekg/freebayes
 
-.. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
   </help>
 </tool>
diff -r 5022cd74093c -r 322df5780b19 freebayes-d291dc763c4c/tool_dependencies.xml
--- a/freebayes-d291dc763c4c/tool_dependencies.xml	Sat Sep 28 06:48:44 2013 -0400
+++ b/freebayes-d291dc763c4c/tool_dependencies.xml	Sat Sep 28 21:18:02 2013 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="freebayes" version="0.9.9_c993c5c07e7673">
+    <package name="freebayes" version="8e44a20fccfe6c5c63f7e8aeb0f53548bf2e2ba7">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
-                <action type="shell_command">git checkout c993c5c07e7673</action>
+                <action type="shell_command">git checkout 8e44a20fccfe6c5c63f7e8aeb0f53548bf2e2ba7</action>
                 <action type="shell_command">git submodule update --recursive</action>
                 <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
                 <action type="move_directory_files">