- changed title to new conda recipe
new conda recipe
Issue #2
resolved
Hi,
I was using
conda install -c bbglab oncodrivefml
Fetching package metadata ...................
Solving package specifications: .
# All requested packages already installed.
# packages in environment at /apps/conda/envs/oncodrive:
#
oncodrivefml 2.0.2 py36_0 bbglab
oncodrivefml -i LUAD_oncodrive_input.tsv1 -e cds.regions.gz -c oncodrivefml.conf --type coding --sequencing wes -o LUAD_oncodrive
23:00:21 INFO: Using HG19 as reference genome
23:00:21 INFO: Running analysis
Parsing elements 'cds.regions.gz': 100%|███████████████████████████████████████████████████████████████| 207139/207139 [00:08<00:00, 24270.52it/s]
23:00:37 INFO: Mapping mutations
* [0 muts]
** [252341 muts]
23:00:44 INFO: Computing signatures
Traceback (most recent call last):
File "/apps/conda/envs/oncodrive/bin/oncodrivefml", line 6, in <module>
sys.exit(oncodrivefml.main.cmdline())
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 382, in cmdline
main(mutations_file, elements_file, output_folder, config_file, samples_blacklist, generate_pickle, override_config)
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 332, in main
analysis.run()
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 194, in run
self.__compute_signature()
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/main.py", line 135, in __compute_signature
save_pickle=save_signature_pickle)
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/signature.py", line 331, in load_signature
signature_dict = compute_signature(signature_function, classifier, collapse, include_mnp)
File "/apps/conda/envs/oncodrive/lib/python3.6/site-packages/oncodrivefml/signature.py", line 224, in compute_signature
logger.debug('Discrepancy in substitution at position %d of chr %s', pos, mut['CHROMOSOME'])
UnboundLocalError: local variable 'pos' referenced before assignment
this error was solved by https://bitbucket.org/bbglab/oncodrivefml/commits/271302acada6300f33eab45d5dae5e8bf238cce9 (thanks Loris for answering my email)
can you please add a new conda receipt for the new version?
Thanks! Tommy
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