comparison amplicon_analysis_pipeline.py @ 37:e832be1635b4 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty

36:c9ed9443f293

        ref_database = "silva"
    elif args.use_homd:
        ref_database = "homd"
    else:
        ref_database = "gg"

    # Executables
    os.mkdir("bin")
    os.environ["PATH"] = os.path.abspath("bin") + \
                         os.pathsep + \
                         os.environ["PATH"]
    print "-- updated PATH: %s" % os.environ["PATH"]
    # Pipeline wants 'vsearch113' but bioconda version is just
    # 'vsearch'
    vsearch = find_executable("vsearch113")
    if vsearch is None:
        vsearch = find_executable("vsearch")
    if vsearch:
        os.symlink(vsearch,os.path.join("bin","vsearch113"))
        print "-- made symlink to %s" % vsearch
    else:
        sys.stderr.write("Missing 'vsearch[113]'\n")
    # Pipeline wants 'fasta-splitter.pl' but bioconda provides
    # 'fasta-splitter'
    fasta_splitter = find_executable("fasta-splitter.pl")
    if fasta_splitter is None:
        fasta_splitter = find_executable("fasta-splitter")
        if os.path.islink(fasta_splitter):
            fasta_splitter = os.path.join(
                os.path.dirname(fasta_splitter),
                os.readlink(fasta_splitter))
    if fasta_splitter:
        os.symlink(fasta_splitter,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
    # 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")
    # 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\t%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:

37:e832be1635b4

        ref_database = "silva"
    elif args.use_homd:
        ref_database = "homd"
    else:
        ref_database = "gg"

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