def __init__(self, configuration=None): """ Init function :param configuration: A dictionary containing parameters that define how the operation should be carried out, which are specific to DpFrEP tool. :type configuration: dict """ Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration) for k, v in self.configuration.items(): if isinstance(v, list): self.configuration[k] = ' '.join(v) # Init variables self.current_dir = os.path.abspath(os.path.dirname(__file__)) self.parent_dir = os.path.abspath(self.current_dir + "/../") self.execution_path = self.configuration.get('execution', '.') if not os.path.isabs(self.execution_path): self.execution_path = os.path.normpath(os.path.join(self.parent_dir, self.execution_path)) self.arguments = dict( [(key, value) for key, value in self.configuration.items() if key not in self.DEFAULT_KEYS] )
def __init__(self, configuration=None): """ Init function """ print("3D JSON Model Indexer") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Init function """ logger.info("BED File Sorter") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Init function """ logger.info("MACS2 Peak Caller") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Init function """ logger.info("TrimGalore FASTQ read trimming") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Init function """ logger.info("BamQC - Bam file stats") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Init function """ logger.info("TCGA Cancer Drivers assessment pipeline") Tool.__init__(self) local_config = configparser.ConfigParser() local_config.read(sys.argv[0] + '.ini') self.docker_tag = local_config.get('tcga_cd','docker_tag') if local_config.has_option('tcga_cd','docker_tag') else 'latest' if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Initialising the function Parameters ---------- configuration: dict """ print("hicup initialising") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Initialise the tool with its configuration Parameters ---------- configuration: dict parameters to run the tool """ logger.info("initialising makeBaitmapTool") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Initialise the tool with the configuration file Parameters ---------- configuration: dict Dictionary containing parameters defining how the tool should work """ Tool.__init__(self) print("Initialising makeDesingFiles") if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Initialise the tool with its configuration. Parameters ---------- configuration : dict a dictionary containing parameters that define how the operation should be carried out, which are specific to each Tool. """ print("BS-Seeker Aligner") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Init function """ logger.info("VRE CWL Workflow runner") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration) # Arrays are serialized for k, v in self.configuration.items(): if isinstance(v, list): self.configuration[k] = ' '.join(v) self.populable_outputs = {}
def __init__(self, configuration=None): """ initialising the function Parameters: ----------- configuration: dict dictionary containing all the arguments and parameters to run the tool """ print("bam2chicago initialising") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Initialise the tool with its configuration. Parameters ---------- configuration : dict a dictionary containing parameters that define how the operation should be carried out, which are specific to each Tool. """ logger.info("Kallisto Quantification") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self, configuration=None): """ Init function """ logger.debug("VRE Progeny runner") Tool.__init__(self) if configuration is None: configuration = {} self.configuration.update(configuration) # Arrays are serialized for k, v in self.configuration.items(): if isinstance(v, list): self.configuration[k] = ' '.join(v) self.progeny = Progeny() self.outputs = dict() self.execution_path = None self.img_path = None
def __init__(self): """ Init function """ print("TADbit full_mapping") Tool.__init__(self)
def __init__(self, configuration=None): """ Init function """ logger.info("OpenEBench VRE Nexflow pipeline runner") Tool.__init__(self) local_config = configparser.ConfigParser() local_config.read(sys.argv[0] + '.ini') # Setup parameters self.nxf_image = local_config.get( 'nextflow', 'docker_image') if local_config.has_option( 'nextflow', 'docker_image') else self.DEFAULT_NXF_IMAGE self.nxf_version = local_config.get( 'nextflow', 'version') if local_config.has_option( 'nextflow', 'version') else self.DEFAULT_NXF_VERSION self.wf_basedir = os.path.abspath( os.path.expanduser( local_config.get('workflows', 'basedir') if local_config. has_option('workflows', 'basedir' ) else self.DEFAULT_WF_BASEDIR)) # Where the external commands should be located self.docker_cmd = local_config.get( 'defaults', 'docker_cmd') if local_config.has_option( 'defaults', 'docker_cmd') else self.DEFAULT_DOCKER_CMD self.git_cmd = local_config.get( 'defaults', 'git_cmd') if local_config.has_option( 'defaults', 'git_cmd') else self.DEFAULT_GIT_CMD # Now, we have to assure the nextflow image is already here docker_tag = self.nxf_image + ':' + self.nxf_version checkimage_params = [ self.docker_cmd, "images", "--format", "{{.ID}}\t{{.Tag}}", docker_tag ] with tempfile.NamedTemporaryFile() as checkimage_stdout: with tempfile.NamedTemporaryFile() as checkimage_stderr: retval = subprocess.call(checkimage_params, stdout=checkimage_stdout, stderr=checkimage_stderr) if retval != 0: # Reading the output and error for the report with open(checkimage_stdout.name, "r") as c_stF: checkimage_stdout_v = c_stF.read() with open(checkimage_stderr.name, "r") as c_stF: checkimage_stderr_v = c_stF.read() errstr = "ERROR: VRE Nextflow Runner failed while checking Nextflow image (retval {}). Tag: {}\n======\nSTDOUT\n======\n{}\n======\nSTDERR\n======\n{}".format( retval, docker_tag, checkimage_stdout_v, checkimage_stderr_v) logger.fatal(errstr) raise Exception(errstr) do_pull_image = os.path.getsize(checkimage_stdout.name) == 0 if do_pull_image: # The image is not here yet pullimage_params = [self.docker_cmd, "pull", docker_tag] with tempfile.NamedTemporaryFile() as pullimage_stdout: with tempfile.NamedTemporaryFile() as pullimage_stderr: retval = subprocess.call(pullimage_params, stdout=pullimage_stdout, stderr=pullimage_stderr) if retval != 0: # Reading the output and error for the report with open(pullimage_stdout.name, "r") as c_stF: pullimage_stdout_v = c_stF.read() with open(pullimage_stderr.name, "r") as c_stF: pullimage_stderr_v = c_stF.read() # It failed! errstr = "ERROR: VRE Nextflow Runner failed while pulling Nextflow image (retval {}). Tag: {}\n======\nSTDOUT\n======\n{}\n======\nSTDERR\n======\n{}".format( retval, docker_tag, pullimage_stdout_v, pullimage_stderr_v) logger.fatal(errstr) raise Exception(errstr) if configuration is None: configuration = {} self.configuration.update(configuration)
def __init__(self): """ Init function """ print("TADbit - Generate TADs") Tool.__init__(self)
def __init__(self): """ Init function """ print("TADbit save adjacency matrix") Tool.__init__(self)