def fill_and_write_instance_config(assnake_db, fna_db_dir, bwa_index_dir,
conda_dir, drmaa_log_dir,
instance_config_location):
'''
Accepts all the necessary config props and dumps them to the provided location as file
:return: location of instance config file if everything is ok, None otherwise
'''
dir_of_this_file = os.path.dirname(os.path.abspath(__file__))
assnake_install_dir = (dir_of_this_file.replace('assnake/commands',
'snake'))
config_template_loc = os.path.join(dir_of_this_file,
'../snake/config_template.yml')
config_template = read_yaml(config_template_loc)
config_template['assnake_db'] = assnake_db
config_template['assnake_install_dir'] = assnake_install_dir
config_template['fna_db_dir'] = fna_db_dir
config_template['bwa_index_dir'] = bwa_index_dir
config_template['conda_dir'] = conda_dir
config_template['drmaa_log_dir'] = drmaa_log_dir
os.makedirs(fna_db_dir, exist_ok=True)
os.makedirs(bwa_index_dir, exist_ok=True)
os.makedirs(conda_dir, exist_ok=True)
os.makedirs(drmaa_log_dir, exist_ok=True)
with open(instance_config_location, 'w+') as file:
_ = yaml.dump(config_template, file, sort_keys=False)
return instance_config_location
def read_assnake_instance_config():
'''
Reads particular assnake instance config. It is stored inside assnake database as config.yaml (Name subject to change).
:return: Returns dict if instance config exists, None otherwise.
'''
# TODO optimize number of times this is called
# print('reading instance config')
internal_config = read_internal_config()
instance_config_loc = internal_config['instance_config_loc']
if os.path.isfile(instance_config_loc):
return read_yaml(instance_config_loc)
else:
return None
def read_internal_config():
'''
Reads the config at ~/.config/assnake/internal_config.yaml and returns as dict
'''
internal_config_loc = os.path.join(str(Path.home()),
'.config/assnake/internal_config.yaml')
if os.path.isfile(internal_config_loc):
internal_config = read_yaml(internal_config_loc)
return internal_config
else:
internal_config_dir = os.path.join(str(Path.home()),
'.config/assnake/')
os.makedirs(internal_config_dir, exist_ok=True)
if not os.path.isfile(internal_config_loc):
with open(internal_config_loc, 'w+') as file:
_ = yaml.dump({'instance_config_loc': 'not_set'},
file,
sort_keys=False)
return {'instance_config_loc': ''}
def cli(ctx):
"""\b
___ ____ ____ _ __ ___ __ __ ____
/ _ | / __/ / __/ / |/ / / _ | / //_/ / __/
/ __ | _\ \ _\ \ / / / __ | / ,< / _/
/_/ |_|/___/ /___/ /_/|_/ /_/ |_|/_/|_| /___/
\b
O---o Welcome to the Assnake, Traveller!
O-o If you found yorself here,
O than you are exploring the land of the MICROBIOME.
o-O Here you can find weapons and spells
o---O that will help you to analyse your data.
O---o The tools that are presented here
O-o are for metagenomics studies on ILLUMINA data.
O You can check quality and preprocess your data,
o-O assemble it, map, bin the contigs,
o---O make taxonomic annotations, functional annotations,
O---o and work with 16s rRNA data.
"""
dir_of_this_file = os.path.dirname(os.path.abspath(__file__))
instance_config = read_assnake_instance_config()
if instance_config is not None:
wc_config = read_yaml(
os.path.join(dir_of_this_file, '../snake/wc_config.yaml'))
ctx.obj = {
'config': instance_config,
'wc_config': wc_config,
'requested_dfs': [],
'requests': [],
'sample_sets': [],
'requested_results': []
}
def from_location(cls,
name,
result_type,
location,
input_type,
additional_inputs=[],
description='',
with_presets=False,
static_files_dir_name='static',
invocation_command=None,
preset_preparation=None,
preset_file_format='json'):
'''
This method is a wrapper for creating an instance of Result class by grabbing the snakefiles and wc_config automatically
from user-provided `location`. How can we make grabbing the location automatic?
:param name: Name of the Result, will also appear as a command name.
:param location: Absolute location where files are stored. We need it in order to grab .smk and wc_config and all other static files.
:param input_type: Type of primary input for this result. Currently we use illumina_sample, illumina_sample_set, illumina_strand_file, illumina_strand_file_set
:param additional_inputs: Any additional inputs for the Result. Usually it would be Database, Reference and their mixes.
:param invocation_command: Users can pass custom invocation commands that will be used in CLI instead of auto-generated ones. Useful for custom logic in CLI.
:param preset_preparation: Functions that tells the Result how to save it's presets to database.
:param preset
:param description: Description of the Result, will also appear as a short help in CLI.
'''
# Find all smk files for Result. This is snakemake workflows.
workflows = glob.glob(os.path.join(location, 'workflow*.smk'))
# Find all wc_config files.
wc_config = os.path.join(location, 'wc_config.yaml')
# Find default config files
default_config = os.path.join(location, 'default_config.yaml')
if len(workflows) == 0: # No workflow files found
print('===', name)
print('No workflow files found')
# Check for config file with wildcards and load.
if os.path.isfile(wc_config):
wc_config = read_yaml(wc_config)
result_wc = wc_config[name + '_wc']
else:
# print('No wc config file found for result', name)
wc_config = {}
result_wc = ''
if os.path.isfile(default_config):
default_config = read_yaml(default_config)
else:
# print('No default_config file found for result', name)
default_config = None
if with_presets:
preset_manager = PresetManager(
dir_in_database=os.path.join('presets', name),
included_presets_dir=os.path.join(location, 'presets'),
static_files_dir_name=static_files_dir_name,
preset_file_format=preset_file_format)
else:
preset_manager = None
x = cls(
name=name,
workflows=workflows,
result_type=result_type,
result_wc=result_wc,
input_type=input_type,
additional_inputs=additional_inputs,
invocation_command=invocation_command,
preset_preparation=preset_preparation,
wc_config=wc_config,
preset_manager=preset_manager,
description=description,
)
return x
def load_wc_config():
dir_of_this_file = os.path.dirname(os.path.abspath(__file__))
return (read_yaml(os.path.join(dir_of_this_file,
'../snake/wc_config.yaml')))
def read_deployed_config(self):
if self.assnake_config is not None:
def_loc = os.path.join(self.assnake_config['assnake_db'], 'module_configs', self.name + '.yaml')
if os.path.isfile(def_loc):
return read_yaml(def_loc)
return None