comparison amplicon_analysis_pipeline.py @ 27:b5e43dfe07ac draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979

26:f0917c340f13

    fasta_splitter = find_executable("fasta-splitter.pl")
    if fasta_splitter is None:
        fasta_splitter = os.readlink(
            find_executable("fasta-splitter"))
    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

        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"]
    # Check for fasta_number.py
    fasta_number = find_executable("fasta_number.py")
    if not fasta_number:
        # Make a link to relabel_fasta.py
        relabel_fasta_path = os.path.join(os.path.dirname(__file__),
                                          "relabel_fasta.py")
        fasta_number_path = os.path.join(os.path.abspath("bin"),
                                         "fasta_number.py")
        os.symlink(relabel_fasta_path,fasta_number_path)
        print "-- linked %s to %s" % (relabel_fasta_path,
                                      fasta_number_path)

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

27:b5e43dfe07ac

    fasta_splitter = find_executable("fasta-splitter.pl")
    if fasta_splitter is None:
        fasta_splitter = os.readlink(
            find_executable("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

        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: