# HG changeset patch
# User peterjc
# Date 1366818730 14400
# Node ID 8bddbb4b2575d298acc303c7da58db8a293b826e
# Parent  c947750f82fbcdcd6a7aacd8e4bb682146b9bec9
Uploaded v0.0.6

diff -r c947750f82fb -r 8bddbb4b2575 tools/sr_assembly/mira.txt
--- a/tools/sr_assembly/mira.txt	Wed Apr 24 11:51:50 2013 -0400
+++ b/tools/sr_assembly/mira.txt	Wed Apr 24 11:52:10 2013 -0400
@@ -44,6 +44,8 @@
 v0.0.5 - Implement the <version_command> tag to record the wrapper
          version and the MIRA version being used.
        - Check using MIRA 3.4 (later versions have a different API)
+v0.0.6 - Tell MIRA to use /tmp for temporary files
+       - Tell MIRA to ignore long read names (otherwise it aborts)
 
 
 Developers
diff -r c947750f82fb -r 8bddbb4b2575 tools/sr_assembly/mira.xml
--- a/tools/sr_assembly/mira.xml	Wed Apr 24 11:51:50 2013 -0400
+++ b/tools/sr_assembly/mira.xml	Wed Apr 24 11:52:10 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.5">
+<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
     <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
 	<version_command interpreter="python">mira.py -v</version_command>
 	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
@@ -37,12 +37,20 @@
 
 ##Output files
 COMMON_SETTINGS
+
+##ignore warnings about long read names
+-MI:somrnl=0
+
 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
 ##Explicitly disable formats we won't use like MAF (reduce IO)
 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
+
 ##remove_rollover_tmps, remove_tmp_directory
 -OUT:rrot=1:rtd=1
 
+##put mira temp directory on local storage                                                                              
+-DI:trt=/tmp
+
     </command>
 	<inputs>
         <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
@@ -124,11 +132,12 @@
 	    <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
 	    <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
 	    <data name="out_log" format="txt" label="MIRA log" />
-    </outputs>
+	</outputs>
 	<tests>
 	</tests>
 	<requirements>
 		<requirement type="python-module">Bio</requirement>
+		<requirement type="binary">mira</requirement>
 	</requirements>
 	<help>