comparison data_manager/interproscan.py @ 3:0df47f8552f6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 01e8e726d711c0685f46d3146e4fe0f2a1306036

2:7776cb18fdf8

            raise RuntimeError("Version '%s' is not valid" % args.version)
        tag = args.version
    else:
        tag = all_tags[-1]

    print("Will download data for InterProScan version: %s" % tag)

    print("Getting MD5 checksum:")
    md5 = requests.get(url=MD5_URL.format(version=tag)).text
    if not re.match(r"^([a-fA-F\d]{32})  interproscan-[0-9]\.[0-9]{2}-[0-9]{2}\.[0-9]-64-bit.tar.gz$", md5):

    print("Done, removing tarball and unneeded files...")
    os.remove(dest_tar)
    shutil.rmtree(os.path.join(output_directory, 'interproscan-%s' % tag))

    print("Running initial_setup.py (index hmm models)...")
    # Write a temp properties file in work dir
    prop_file_src = os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'interproscan.properties')
    with open(prop_file_src, 'r') as prop:
        prop_content = prop.read()
    prop_content = re.sub(r'^data\.directory=.*$', 'data.directory=%s' % os.path.join(output_directory, 'data'), prop_content, flags=re.M)
    with open('interproscan.properties', 'w') as prop:
        prop.write(prop_content)
    # Run the index command
    cmd_args = [os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'initial_setup.py')]
    proc = subprocess.Popen(args=cmd_args, shell=False)
    out, err = proc.communicate()
    print(out)
    print(err, file=sys.stderr)
    return_code = proc.wait()
    if return_code:
        print("Error running initial_setup.py.", file=sys.stderr)
        sys.exit(return_code)

    data_manager_dict["data_tables"][args.datatable_name].append(
        dict(
            value=tag,

3:0df47f8552f6

            raise RuntimeError("Version '%s' is not valid" % args.version)
        tag = args.version
    else:
        tag = all_tags[-1]

    setup_script = 'initial_setup.py'
    sub_version = re.match(r"^[0-9]\.([0-9]{2})-[0-9]{2}\.[0-9]$", tag)
    if sub_version and len(sub_version.groups()) == 1 and int(sub_version.group(1)) >= 58:
        # The setup script was renamed in 5.58
        setup_script = 'setup.py'
    else:
        raise RuntimeError("Sorry, this data manager can only download data for InterProScan >= 5.58-91.0. Use the 0.0.2 version for older versions of InterProScan.")

    print("Will download data for InterProScan version: %s" % tag)

    print("Getting MD5 checksum:")
    md5 = requests.get(url=MD5_URL.format(version=tag)).text
    if not re.match(r"^([a-fA-F\d]{32})  interproscan-[0-9]\.[0-9]{2}-[0-9]{2}\.[0-9]-64-bit.tar.gz$", md5):

    print("Done, removing tarball and unneeded files...")
    os.remove(dest_tar)
    shutil.rmtree(os.path.join(output_directory, 'interproscan-%s' % tag))

    print("Running {} (index hmm models)...".format(setup_script))
    # Write a temp properties file in work dir
    prop_file_src = os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), 'interproscan.properties')
    with open(prop_file_src, 'r') as prop:
        prop_content = prop.read()
    prop_content = re.sub(r'^data\.directory=.*$', 'data.directory=%s' % os.path.join(output_directory, 'data'), prop_content, flags=re.M)
    with open('interproscan.properties', 'w') as prop:
        prop.write(prop_content)
    # Run the index command
    cmd_args = [os.path.join(os.path.dirname(os.path.realpath(shutil.which("interproscan.sh"))), setup_script), 'interproscan.properties']
    proc = subprocess.Popen(args=cmd_args, shell=False)
    out, err = proc.communicate()
    print(out)
    print(err, file=sys.stderr)
    return_code = proc.wait()
    if return_code:
        print("Error running {}.".format(setup_script), file=sys.stderr)
        sys.exit(return_code)

    data_manager_dict["data_tables"][args.datatable_name].append(
        dict(
            value=tag,