src/toil_lib/abstractPipelineWrapper.py
def run(cls, name, desc):
        """
        Prepares and runs the pipeline. Note this method must be invoked both from inside a
        Docker container and while the docker daemon is reachable.

        :param str name: The name of the command to start the workflow.
        :param str desc: The description of the workflow.
        """
        wrapper = cls(name, desc)
        mount_path = wrapper._get_mount_path()
        # prepare parser
        arg_parser = wrapper._create_argument_parser()
        wrapper._extend_argument_parser(arg_parser)
        # prepare config file
        empty_config = wrapper.__get_empty_config()
        config_yaml = ruamel.yaml.load(empty_config)
        wrapper.__populate_parser_from_config(arg_parser, config_yaml)
        args = arg_parser.parse_args()
        for k,v in vars(args).items():
            k = k.replace('_', '-')
            if k in config_yaml:
                config_yaml[k] = v
        config_path = wrapper._get_config_path()
        with open(config_path, 'w') as writable:
            ruamel.yaml.dump(config_yaml, stream=writable)
        # prepare workdir
        workdir_path = os.path.join(mount_path, 'Toil-' + wrapper._name)
        if os.path.exists(workdir_path):
            if args.restart:
                 log.info('Reusing temporary directory: %s', workdir_path)
            else:
                raise UserError('Temporary directory {} already exists. Run with --restart '
                                'option or remove directory.'.format(workdir_path))
        else:
            os.makedirs(workdir_path)
            log.info('Temporary directory created: %s', workdir_path)

        command = wrapper._create_pipeline_command(args, workdir_path, config_path)
        wrapper._extend_pipeline_command(command, args)
        # run command
        try:
            subprocess.check_call(command)
        except subprocess.CalledProcessError as e:
            print(e, file=sys.stderr)
        finally:
            stat = os.stat(mount_path)
            log.info('Pipeline terminated, changing ownership of output files in %s from root to '
                     'uid %s and gid %s.', mount_path, stat.st_uid, stat.st_gid)
            chown_command = ['chown', '-R', '%s:%s' % (stat.st_uid, stat.st_gid), mount_path]
            subprocess.check_call(chown_command)
            if args.no_clean:
                log.info('Flag "--no-clean" was used, therefore %s was not deleted.', workdir_path)
            else:
                log.info('Cleaning up temporary directory: %s', workdir_path)
                shutil.rmtree(workdir_path)
def run(cls, name, desc):
        """
        Prepares and runs the pipeline. Note this method must be invoked both from inside a
        Docker container and while the docker daemon is reachable.

        :param str name: The name of the command to start the workflow.
        :param str desc: The description of the workflow.
        """
        wrapper = cls(name, desc)
        mount_path = wrapper._get_mount_path()
        # prepare parser
        arg_parser = wrapper._create_argument_parser()
        wrapper._extend_argument_parser(arg_parser)
        # prepare config file
        empty_config = wrapper.__get_empty_config()
        config_yaml = ruamel.yaml.load(empty_config)
        wrapper.__populate_parser_from_config(arg_parser, config_yaml)
        args = arg_parser.parse_args()
        for k,v in vars(args).items():
            k = k.replace('_', '-')
            if k in config_yaml:
                config_yaml[k] = v
        config_path = wrapper._get_config_path()
        with open(config_path, 'w') as writable:
            ruamel.yaml.dump(config_yaml, stream=writable)
        # prepare workdir
        workdir_path = os.path.join(mount_path, 'Toil-' + wrapper._name)
        if os.path.exists(workdir_path):
            if args.restart:
                 log.info('Reusing temporary directory: %s', workdir_path)
            else:
                raise UserError('Temporary directory {} already exists. Run with --restart '
                                'option or remove directory.'.format(workdir_path))
        else:
            os.makedirs(workdir_path)
            log.info('Temporary directory created: %s', workdir_path)

        command = wrapper._create_pipeline_command(args, workdir_path, config_path)
        wrapper._extend_pipeline_command(command, args)
        # run command
        try:
            subprocess.check_call(command)
        except subprocess.CalledProcessError as e:
            print(e, file=sys.stderr)
        finally:
            stat = os.stat(mount_path)
            log.info('Pipeline terminated, changing ownership of output files in %s from root to '
                     'uid %s and gid %s.', mount_path, stat.st_uid, stat.st_gid)
            chown_command = ['chown', '-R', '%s:%s' % (stat.st_uid, stat.st_gid), mount_path]
            subprocess.check_call(chown_command)
            if args.no_clean:
                log.info('Flag "--no-clean" was used, therefore %s was not deleted.', workdir_path)
            else:
                log.info('Cleaning up temporary directory: %s', workdir_path)
                shutil.rmtree(workdir_path)
Prepares and runs the pipeline. Note this method must be invoked both from inside a
        Docker container and while the docker daemon is reachable.

        :param str name: The name of the command to start the workflow.
        :param str desc: The description of the workflow.