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Lsf config #1

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Lsf config #1

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f3ee135
update get_lsf_config to take path to config file
DerekLiu35 Aug 7, 2024
5b16612
add default path
DerekLiu35 Aug 7, 2024
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24 changes: 16 additions & 8 deletions snakemake_executor_plugin_lsf/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -528,14 +528,22 @@ def get_default_queue(self, job):
return ""

@staticmethod
def get_lsf_config():
lsf_config_raw = subprocess.run(
"badmin showconf mbd", shell=True, capture_output=True, text=True
)

lsf_config_lines = lsf_config_raw.stdout.strip().split("\n")
lsf_config_tuples = [tuple(x.strip().split(" = ")) for x in lsf_config_lines]
lsf_config = {x[0]: x[1] for x in lsf_config_tuples[1:]}
def get_lsf_config(path="/etc/lsf.conf"):
try:
lsf_config_raw = subprocess.run(
"badmin showconf mbd", shell=True, capture_output=True, text=True, check=True
).stdout
except subprocess.CalledProcessError:
print("Could not get LSF config from badmin showconf mbd")
config_file_path = os.environ.get('LSF_CONFIG_FILE', path)
try:
with open(config_file_path, 'r') as file:
lsf_config_raw = file.read()
except FileNotFoundError:
raise FileNotFoundError(f"LSF config file not found at {config_file_path}")
lsf_config_lines = lsf_config_raw.strip().split("\n")
lsf_config_tuples = [tuple(x.strip().split("=")) for x in lsf_config_lines if len(tuple(x.strip().split("=")))==2]
lsf_config = {x[0]: x[1] for x in lsf_config_tuples}
clusters = subprocess.run(
"lsclusters", shell=True, capture_output=True, text=True
)
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