# HG changeset patch
# User peterjc
# Date 1400669766 14400
# Node ID 8487d70e82aaf0b73c0bb99b16fb6c8ff558dd32
# Parent  381aa262c8cbe926ea2006cf3ff778b3da3f7b12
Uploaded v0.0.3 preview 1, target MIRA v4.0.2

diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/README.rst
--- a/tools/mira4/README.rst	Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/README.rst	Wed May 21 06:56:06 2014 -0400
@@ -22,7 +22,7 @@
 
 This should be straightforward. Via the Tool Shed, Galaxy should automatically
 install the 'mira' datatype, samtools, and download and install the precompiled
-binary for MIRA v4.0 for the Galaxy wrapper, and run any tests.
+binary for MIRA v4.0.2 for the Galaxy wrapper, and run any tests.
 
 For MIRA 4, the Galaxy wrapper has been split in two, allowing separate
 cluster settings for de novo usage (high RAM) and mapping (lower RAM).
@@ -56,7 +56,7 @@
   <tool file="mira4/mira4_de_novo.xml" />
   <tool file="mira4/mira4_mapping.xml" />
 
-You will also need to install MIRA, we used version 4.0, and define the
+You will also need to install MIRA, we used version 4.0.2, and define the
 environment variable ``$MIRA4`` pointing at the folder containing the binaries.
 See:
 
@@ -85,11 +85,12 @@
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial version (prototype for MIRA 4.0 RC4, based on wrapper for v3.4)
 v0.0.2  - Include BAM output (using ``miraconvert`` and ``samtools``).
-        - Updated to target MIRA 4.0
+        - Updated to target MIRA 4.0.1
         - Simplified XML to apply input format to output data.
         - Sets temporary folder at run time to respect environment variables
           (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
           previously hard coded as ``/tmp``.
+v0.0.3  - Updated to target MIRA 4.0.2
 ======= ======================================================================
 
 
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4.py
--- a/tools/mira4/mira4.py	Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4.py	Wed May 21 06:56:06 2014 -0400
@@ -91,9 +91,12 @@
     #but could be followed by a space in future...
     text = text.replace("-DI:trt=/tmp", "-DI:trt=" + tempfile.gettempdir())
 
+    #Want to try to ensure this gets written to disk before MIRA attempts
+    #to open it - any networked file system may impose a delay...
     handle = open(manifest, "w")
     handle.write(text)
     handle.flush()
+    os.fsync(handle.fileno())
     handle.close()
 
 
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4_bait.xml
--- a/tools/mira4/mira4_bait.xml	Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4_bait.xml	Wed May 21 06:56:06 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.2">
+<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.3">
     <description>Filter reads using kmer matches</description>
     <requirements>
         <requirement type="binary">mirabait</requirement>
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4_de_novo.xml
--- a/tools/mira4/mira4_de_novo.xml	Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4_de_novo.xml	Wed May 21 06:56:06 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.2">
+<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.3">
     <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -82,7 +82,7 @@
         <configfile name="manifest">
 project = MIRA
 job = denovo,${job_type},${job_quality}
-parameters = -NW:cmrnl=no -DI:trt=/tmp
+parameters = -NW:cmrnl=no -DI:trt=/tmp -OUT:orc=no
 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
 ## can be useful for repeatability of assemblies and bug hunting.
 ## This is overriden by the command line -t switch which is easier
@@ -95,6 +95,9 @@
 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
 ## point to a local hard drive (not something like NFS on network).
 ## We replace /tmp with an environment variable via mira4.py
+##
+## -OUT:orc=no is short for -OUTPUT:output_result_caf=no 
+## which turns off an output file we don't want anyway.
 
 #for $rg in $read_group
 
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/mira4_mapping.xml
--- a/tools/mira4/mira4_mapping.xml	Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/mira4_mapping.xml	Wed May 21 06:56:06 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.2">
+<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.3">
     <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -80,7 +80,7 @@
         <configfile name="manifest">
 project = MIRA
 job = mapping,${job_type},${job_quality}
-parameters = -NW:cmrnl=no -DI:trt=/tmp
+parameters = -NW:cmrnl=no -DI:trt=/tmp -OUT:orc=no
 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
 ## can be useful for repeatability of assemblies and bug hunting.
 ## This is overriden by the command line -t switch which is easier
@@ -93,6 +93,9 @@
 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
 ## point to a local hard drive (not something like NFS on network).
 ## We replace /tmp with an environment variable via mira4.py
+##
+## -OUT:orc=no is short for -OUTPUT:output_result_caf=no
+## which turns off an output file we don't want anyway.
 
 ##This bar goes into the manifest as a comment line
 #------------------------------------------------------------------------------
diff -r 381aa262c8cb -r 8487d70e82aa tools/mira4/tool_dependencies.xml
--- a/tools/mira4/tool_dependencies.xml	Tue Mar 25 07:37:50 2014 -0400
+++ b/tools/mira4/tool_dependencies.xml	Wed May 21 06:56:06 2014 -0400
@@ -1,14 +1,14 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="36aa94676939" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="MIRA" version="4.0">
         <install version="1.0">
             <actions_group>
                 <!-- Download the binaries for MIRA compatible with 64-bit OSX. -->
                 <actions architecture="x86_64" os="darwin">
-                    <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_darwin13.0.0_x86_64_static.tar.bz2</action>
+                    <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_darwin13.1.0_x86_64_static.tar.bz2</action>
                     <action type="move_directory_files">
                          <source_directory>bin</source_directory>
                          <destination_directory>$INSTALL_DIR</destination_directory>
@@ -16,7 +16,7 @@
                 </actions>
                 <!-- Download the binaries for MIRA compatible with 64-bit Linux. -->
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2</action>
+                    <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0.2_linux-gnu_x86_64_static.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>bin</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
@@ -43,7 +43,7 @@
             </actions_group>
         </install>
         <readme>
-Downloads MIRA v4.0 from Sourceforge, requesting Bastien's precompiled binaries
+Downloads MIRA v4.0.2 from Sourceforge, requesting Bastien's precompiled binaries
 for 64 bit (x86_64) Linux or Mac OS X. Other platforms where compilation from
 source would be required (e.g. 32 bit Linux) are not supported by this automated
 installation script.