--- a/tools/mira4/mira4.py	Mon Oct 21 12:01:47 2013 -0400
+++ b/tools/mira4/mira4.py	Fri Oct 25 07:18:38 2013 -0400
@@ -31,8 +31,14 @@
     return ver.split("\n", 1)[0]
 
 
-os.environ["PATH"] = "/mnt/galaxy/downloads/mira_4.0rc4_linux-gnu_x86_64_static/bin/:%s" % os.environ["PATH"]
-mira_binary = "mira"
+try:
+    mira_path = os.environ["MIRA4"]
+except ImportError:
+    stop_err("Environment variable $MIRA4 not set")
+mira_binary = os.path.join(mira_path, "mira")
+if not os.path.isfile(mira_binary):
+    stop_err("Missing mira under $MIRA4, %r" % mira_binary)
+
 mira_ver = get_version(mira_binary)
 if not mira_ver.strip().startswith("4.0"):
     stop_err("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
@@ -40,6 +46,27 @@
     print "%s, MIRA wrapper version %s" % (mira_ver, WRAPPER_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()
+
+    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."""
@@ -102,6 +129,8 @@
 name = "MIRA"
 manifest, out_maf, out_fasta, out_log = sys.argv[1:5]
 
+fix_threads(manifest)
+
 start_time = time.time()
 #cmd_list =sys.argv[8:]
 cmd_list = [mira_binary, manifest]