comparison amplicon_analysis_pipeline.py @ 21:092e39db5f59 draft

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

20:8d8aad8752f9

        # 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")

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

21:092e39db5f59

        # 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")
    # 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"
    pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
    if args.forward_pcr_primer: