charcoal
charcoal copied to clipboard
print nice error when can't find config file
current output is not super user-friendly :)
charcoal run orthodb.conf -n
Traceback (most recent call last):
File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/io.py", line 1372, in _load_configfile
with open(configpath) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'orthodb.conf'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ntpierce/miniconda3/envs/charcoal/bin/snakemake", line 8, in <module>
sys.exit(main())
File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/__init__.py", line 2252, in main
success = snakemake(
File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/__init__.py", line 454, in snakemake
overwrite_config.update(load_configfile(f))
File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/io.py", line 1402, in load_configfile
config = _load_configfile(configpath)
File "/home/ntpierce/miniconda3/envs/charcoal/lib/python3.8/site-packages/snakemake/io.py", line 1397, in _load_configfile
raise WorkflowError("{} file {} not found.".format(filetype, configpath))
snakemake.exceptions.WorkflowError: Config file orthodb.conf not found.
Error in snakemake invocation: Command '['snakemake', '-s', '/home/ntpierce/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-n', '--configfile', '/home/ntpierce/charcoal/charcoal/conf/defaults.conf', '/home/ntpierce/charcoal/charcoal/conf/system.conf', 'orthodb.conf']' returned non-zero exit status 1.