# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1377878186 18000
# Node ID a34ce2b18877cdd9b81bd1dde479dbf05c69fcec
# Parent  d4ce07eb63bdecfa845e9752435802de4289672b
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie

diff -r d4ce07eb63bd -r a34ce2b18877 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 20 09:17:14 2013 -0400
+++ b/tool_dependencies.xml	Fri Aug 30 10:56:26 2013 -0500
@@ -1,21 +1,13 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="trinityrnaseq" version="2013-02-25">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/trinityrnaseq/files/trinityrnaseq_r2013-02-25.tgz</action>
-                <action type="shell_command">make</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
+    <package name="trinityrnaseq" version="2013_08_14">
+        <repository changeset_revision="df23c0ef83a6" name="package_trinityrnaseq_2013_08_14" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.18">
+        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="1.0.0">
+        <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
 
diff -r d4ce07eb63bd -r a34ce2b18877 trinityrnaseq.xml
--- a/trinityrnaseq.xml	Wed Mar 20 09:17:14 2013 -0400
+++ b/trinityrnaseq.xml	Fri Aug 30 10:56:26 2013 -0500
@@ -1,8 +1,10 @@
-<tool id="trinityrnaseq" name="Trinity" version="0.0.1">
+<tool id="trinityrnaseq" name="Trinity" version="0.0.2">
     <!-- Written by Jeremy Goecks, now maintained here by bhaas -->
     <description>De novo assembly of RNA-Seq data Using Trinity</description>
     <requirements>
-        <requirement type="package" version="2013-02-25">trinityrnaseq</requirement>
+        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+        <requirement type="package" version="1.0.0">bowtie</requirement>
     </requirements>
     <command>
         Trinity.pl --JM $JM --CPU $CPU
@@ -41,7 +43,7 @@
 	
                 
         ## direct to output
-        > $trinity_log 2>&amp;1
+        | tee $trinity_log | grep 'Error'
  
     </command>
     <inputs>
@@ -109,6 +111,14 @@
     </inputs>
     <stdio>
         <exit_code range="1:"  level="fatal"   description="Faiiled" />
+        <regex match="command not found" 
+               source="both" 
+               level="fatal" 
+               description="Trinity.pl not found" />
+        <regex match="Error" 
+               source="both" 
+               level="fatal" 
+               description="A trinity process failed" />
     </stdio>
     <outputs>
         <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />