diff amplicon_analysis_pipeline.py @ 21:092e39db5f59 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit bae32168fbfd40305a4768b889a8e7689e5987e3-dirty

--- a/amplicon_analysis_pipeline.py	Tue Jul 03 09:33:34 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Wed Jul 04 05:57:44 2018 -0400
@@ -225,6 +225,15 @@
         print "-- set RDP_JAR_PATH: %s" % os.environ["RDP_JAR_PATH"]
     else:
         sys.stderr.write("Missing 'rdp_classifier.jar'\n")
+    # Set up qiime_config file
+    qiime_config_file = os.path.abspath("qiime_config")
+    with open(qiime_config_file,'w') as qiime_config:
+        # Set qiime_scripts_dir
+        qiime_config.write("qiime_scripts_dir: %s" %
+                           os.path.dirname(
+                               find_executable("single_rarefaction.py")))
+    os.environ["QIIME_CONFIG_FP"] = qiime_config_file
+    print "-- set QIIME_CONFIG_FP: %s" % os.environ["QIIME_CONFIG_FP"]
 
     # Construct the pipeline command
     print "Amplicon analysis: constructing pipeline command"