comparison amplicon_analysis_pipeline.py @ 18:877d53e2d963 draft

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

17:e1ba19551395

    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_classifier = os.path.normpath(
            os.path.join(os.path.dirname(rdp_classifier),
                         "..",
                         "share",
                         "rdp_classifier",
                         "rdp_classifier.jar"))
    if rdp_classifier and os.path.exists(rdp_classifier):
        os.environ["RDP_JAR_PATH"] = rdp_classifier
        print "-- set RDP_JAR_PATH: %s" % os.environ["RDP_JAR_PATH"]
    else:
        sys.stderr.write("Missing 'rdp_classifier.jar'\n")

    # Construct the pipeline command

18:877d53e2d963

    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
    # 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),
                         "..",
                         "share",
                         "rdp_classifier",
                         "rdp_classifier.jar"))
    if rdp_classifier and os.path.exists(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")

    # Construct the pipeline command