Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 18:877d53e2d963 draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit af3afa7bd2c2441074879938cd93d9965908bbc7-dirty
| author | pjbriggs |
|---|---|
| date | Tue, 03 Jul 2018 08:22:44 -0400 |
| parents | e1ba19551395 |
| children | 52052235644b |
| files | amplicon_analysis_pipeline.py |
| diffstat | 1 files changed, 16 insertions(+), 1 deletions(-) [+] |
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--- a/amplicon_analysis_pipeline.py Tue Jul 03 07:20:12 2018 -0400 +++ b/amplicon_analysis_pipeline.py Tue Jul 03 08:22:44 2018 -0400 @@ -197,8 +197,10 @@ # 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 + # which is a link to the 'share/rdp_classifier-<VERSION>/' dir rdp_classifier = find_executable("rdp_classifier") if rdp_classifier: + # Generate expected path to JAR file rdp_classifier = os.path.normpath( os.path.join(os.path.dirname(rdp_classifier), "..", @@ -206,7 +208,20 @@ "rdp_classifier", "rdp_classifier.jar")) if rdp_classifier and os.path.exists(rdp_classifier): - os.environ["RDP_JAR_PATH"] = rdp_classifier + # Get real directory (which contains version) + rdp_classifier_dir = os.readlink( + os.path.dirname(rdp_classifier)) + # Extract the version + rdp_version = '-'.join(os.path.basename( + rdp_classifier_dir).split('-')[1:]) + # Make a symlink to JAR file with version in the name + rdp_jar_path = os.path.join(os.path.abspath("bin"), + "rdp_classifier-%s.jar" % + rdp_version) + os.symlink(rdp_classifier,rdp_jar_path) + print "-- made symlink to %s" % rdp_classifier + # Set the RDP_JAR_PATH env var + os.environ["RDP_JAR_PATH"] = rdp_jar_path print "-- set RDP_JAR_PATH: %s" % os.environ["RDP_JAR_PATH"] else: sys.stderr.write("Missing 'rdp_classifier.jar'\n")