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MorrellLAB / BAD_Mutations

Deleterious mutation prediction pipeline
MIT License
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BioPython check for fetch #6

Open mojaveazure opened 9 years ago

mojaveazure commented 9 years ago

When fetching, it checks for BioPython being installed. On MSI's setup, this breaks the script as it won't fetch on LAB and LOGIN doesn't have BioPython readily available.

mojaveazure commented 9 years ago

Using the latest version from GitHub: hoffmanp@login02 [~/sandbox/LRT_Pipeline/LRT] % ./LRT_Predict.py fetch Traceback (most recent call last): File "./LRT_Predict.py", line 36, in from lrt_predict.Blast import blast_search File "/panfs/roc/groups/9/morrellp/hoffmanp/sandbox/LRT_Pipeline/LRT/lrt_predict/Blast/blast_search.py", line 10, in from Bio.Blast.Applications import NcbitblastxCommandline ImportError: No module named Bio.Blast.Applications

ChaochihL commented 8 years ago

Not able to run fetch on login where we have internet access because it requires BioPython.

TomJKono commented 8 years ago

You should be able to run this package from one of the lab nodes. I'm running the 'fetch' routine right now and it is downloading CDS files.

TomJKono commented 8 years ago

At least ensembl