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cambiotraining / bacterial-genomics

Course materials for "Working with Bacterial Genomes"
https://cambiotraining.github.io/bacterial-genomics/
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Install pandas in base environment #15

Closed bsalehe closed 10 months ago

bsalehe commented 10 months ago

Hi @tavareshugo and @avantonder. I wonder if we could install pandas in the base or in its own env as many other python scripts depend on the pandas downstream for instances seqtk_parser.py or merge_pneumo_data.py. As I have finished testing all scripts for all three isolates, I was consistently getting the pandas package not found error when I ran these scripts. I had to activate seqtk env which seems to have pandas installed to be able to run the scripts.

Thanks

avantonder commented 10 months ago

Might not be a bad idea. In the material I've explicitly stated that the tb-profiler environment needs to be activated as it contains pandas. I may have added pandas after I provided the scripts but it wouldn't be that difficult to update the instances?

tavareshugo commented 10 months ago

Yes, we can still update software. I'll make a note to Paul

tavareshugo commented 10 months ago

Fixed in 0606e1e899627aee13e0807ee57184ba1a8d0fb3