comparison amplicon_analysis_pipeline.py @ 15:07b04a63abf1 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit af3afa7bd2c2441074879938cd93d9965908bbc7-dirty

14:ed175a4b247f

    if fasta_splitter:
        os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl"))
        print "-- made symlink to %s" % fasta_splitter
    else:
        sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")

    # Construct the pipeline command
    print "Amplicon analysis: constructing pipeline command"
    pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
    if args.forward_pcr_primer:

15:07b04a63abf1

    if fasta_splitter:
        os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl"))
        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"
    pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
    if args.forward_pcr_primer: