Merge pull request #425 from galaxyproject/tophat_update

Tophat2 update

Author: bgruening

tools/tophat2/tool_dependencies.xml

@@ -1,5 +1,4 @@
-<tool id="tophat2" name="TopHat" version="2.1.0">
-    <!-- Wrapper compatible with Tophat version 2.0.0+ -->
+<tool id="tophat2" name="TopHat" version="2.1.1">
     <description>Gapped-read mapper for RNA-seq data</description>
     <macros>
       <import>tophat_macros.xml</import>
@@ -33,8 +32,8 @@
       </macro>
     </macros>
     <requirements>
-        <requirement type="package" version="2.2.5">bowtie2</requirement>
-        <requirement type="package" version="2.1.0">tophat</requirement>
+        <requirement type="package" version="2.2.8">bowtie2</requirement>
+        <requirement type="package" version="2.1.1">tophat</requirement>
     </requirements>
     <stdio>
         <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>