Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 15:07b04a63abf1 draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit af3afa7bd2c2441074879938cd93d9965908bbc7-dirty
| author | pjbriggs |
|---|---|
| date | Tue, 03 Jul 2018 07:09:34 -0400 |
| parents | ed175a4b247f |
| children | 4bd582d23d4e |
| files | amplicon_analysis_pipeline.py |
| diffstat | 1 files changed, 16 insertions(+), 0 deletions(-) [+] |
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--- 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"