This patch twists QIIME's arm to accept running a newer version
of the RDP classifier by setting RDP_JAR_VERSION_OK, which is done
by the QIIME wrapper.
This is a nasty hack and hopefully the patch can be dropped for QIIME 1.6
--- a/qiime/assign_taxonomy.py
+++ b/qiime/assign_taxonomy.py
@@ -65,14 +65,20 @@ def validate_rdp_version(rdp_jarpath=Non
             "http://qiime.org/install/install.html#rdp-install"
             )
 
-    rdp_jarname = os.path.basename(rdp_jarpath)
-    version_match = re.search("\d\.\d", rdp_jarname)
-    if version_match is None:
-        raise RuntimeError(
-            "Unable to detect RDP Classifier version in file %s" % rdp_jarname
-            )
+    #Patch for Bio-Linux/Debian.  Allow us to reassure QIIME about the version
+    #of RDP Classifier using an environment variable.
+    if os.getenv('RDP_JAR_VERSION_OK') is not None :
+	version = os.getenv('RDP_JAR_VERSION_OK')
+    else :
+	rdp_jarname = os.path.basename(rdp_jarpath)
+	version_match = re.search("\d\.\d", rdp_jarname)
+	if version_match is None:
+	    raise RuntimeError(
+		"Unable to detect RDP Classifier version in file %s" % rdp_jarname
+		)
+
+	version = float(version_match.group())
 
-    version = float(version_match.group())
     if version < 2.1:
         raise RuntimeError(
             "RDP Classifier does not look like version 2.2 or greater."
--- a/scripts/assign_taxonomy.py
+++ b/scripts/assign_taxonomy.py
@@ -301,6 +301,11 @@ def main():
         params['training_data_properties_fp'] = opts.training_data_properties_fp
         params['max_memory'] = "%sM" % opts.rdp_max_memory
 
+	#Record actual RDP version.  This shouldn't fail as it was called once
+	#already.
+	params['real_rdp_version'] = str(validate_rdp_version())
+
+
     elif assignment_method == 'rtax':
        params['id_to_taxonomy_fp'] = opts.id_to_taxonomy_fp
        params['reference_sequences_fp'] = opts.reference_seqs_fp
