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)
