# HG changeset patch
# User pjbriggs
# Date 1530616174 14400
# Node ID 07b04a63abf138f7913dc9eb1dbd1fdc89672af3
# Parent  ed175a4b247f68d4759bc456cda067fadd793377
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit af3afa7bd2c2441074879938cd93d9965908bbc7-dirty

diff -r ed175a4b247f -r 07b04a63abf1 amplicon_analysis_pipeline.py
--- a/amplicon_analysis_pipeline.py	Mon Jun 18 10:08:03 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Tue Jul 03 07:09:34 2018 -0400
@@ -194,6 +194,22 @@
         print "-- made symlink to %s" % fasta_splitter
     else:
         sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")
+    # Qiime 1.8.0 wants 'RDP_JAR_PATH' env var to point to
+    # the rdp_classifier.jar file
+    # biconda provides this in the 'share/rdp_classifier/' dir
+    rdp_classifier = find_executable("rdp_classifier")
+    if rdp_classifier:
+        rdp_classifer = os.path.normpath(
+            os.path.join(os.path.dirname(rdp_classifer),
+                         "..",
+                         "share",
+                         "rdp_classifier",
+                         "rdp_classifier.jar"))
+    if rdp_classifier and os.path.exists(os.path.join):
+        os.environ["RDP_JAR_PATH"] = rdp_classifer
+        print "-- set RDP_JAR_PATH: %s" % os.environ["RDP_JAR_PATH"]
+    else:
+        sys.stderr.write("Missing 'rdp_classifier.jar'\n")
 
     # Construct the pipeline command
     print "Amplicon analysis: constructing pipeline command"