# HG changeset patch
# User peterjc
# Date 1386674953 18000
# Node ID 02350bef2e9910e32bdb27400c4ee866fac2afb2
# Parent  79759fdec6cb59f5636d384a2f1847cf3db74c71
Uploaded v0.0.2 preview 3, correction regression in URL

diff -r 79759fdec6cb -r 02350bef2e99 tools/mira4/README.rst
--- a/tools/mira4/README.rst	Tue Dec 10 06:26:19 2013 -0500
+++ b/tools/mira4/README.rst	Tue Dec 10 06:29:13 2013 -0500
@@ -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 RC4, and define the
+You will also need to install MIRA, we used version 4.0 RC5, and define the
 environment variable ``$MIRA4`` pointing at the folder containing the binaries.
 See:
 
@@ -85,6 +85,7 @@
 ------- ----------------------------------------------------------------------
 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 RC5
 ======= ======================================================================
 
 
diff -r 79759fdec6cb -r 02350bef2e99 tools/mira4/mira4.py
--- a/tools/mira4/mira4.py	Tue Dec 10 06:26:19 2013 -0500
+++ b/tools/mira4/mira4.py	Tue Dec 10 06:29:13 2013 -0500
@@ -57,27 +57,13 @@
         print "WARNING: miraconvert %s" % mira_convert_ver
     sys.exit(0)
 
-def fix_threads(manifest):
-    """Tweak the manifest to alter the number of threads."""
-    try:
-        threads = int(os.environ.get("GALAXY_SLOTS", "1"))
-    except ValueError:
-        threads = 1
-    assert 1 <= threads 
-    if threads == 1:
-        #Nothing to do...
-        return
 
-    handle = open(manifest)
-    text = handle.read()
-    handle.close()
+try:
+    threads = int(os.environ.get("GALAXY_SLOTS", "1"))
+except ValueError:
+    threads = 1
+assert 1 <= threads, threads
 
-    text = text.replace(" -GE:not=1 ", " -GE:not=%i " % threads)
-
-    handle = open(manifest, "w")
-    handle.write(text)
-    handle.flush()
-    handle.close()
 
 def log_manifest(manifest):
     """Write the manifest file to stderr."""
@@ -150,11 +136,9 @@
 name = "MIRA"
 manifest, out_maf, out_bam, out_fasta, out_log = sys.argv[1:]
 
-fix_threads(manifest)
-
 start_time = time.time()
 #cmd_list =sys.argv[8:]
-cmd_list = [mira_binary, manifest]
+cmd_list = [mira_binary, "-t", str(threads), manifest]
 cmd = " ".join(cmd_list)
 
 assert os.path.isdir(temp)
diff -r 79759fdec6cb -r 02350bef2e99 tools/mira4/tool_dependencies.xml
--- a/tools/mira4/tool_dependencies.xml	Tue Dec 10 06:26:19 2013 -0500
+++ b/tools/mira4/tool_dependencies.xml	Tue Dec 10 06:29:13 2013 -0500
@@ -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_4.0rc4_linux-gnu_x86_64_static.tar.bz2</action>
+                    <action type="download_by_url">https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0rc5_linux-gnu_x86_64_static.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>bin</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>