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cambiotraining / bacterial-genomics

Course materials for "Working with Bacterial Genomes"
https://cambiotraining.github.io/bacterial-genomics/
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ModuleNotFoundError: No module named 'pandas' - when running "merge_tb_data.py" #13

Closed bsalehe closed 7 months ago

bsalehe commented 7 months ago

Hi @avantonder and @tavareshugo I am trying to run merge_tb_data.py. The command is python scripts/merge_tb_data.py -s sample_info.csv -t preprocessed/tb-profiler/Nam_TB.txt. I am experiencing this error:-

Traceback (most recent call last): File "/home/ubuntu/Course_Materials/M_tuberculosis/scripts/merge_tb_data.py", line 7, in import pandas as pd

I tried to change two conda environments accordingly which seem to have pandas; tb-profiler and seqtk based on the instructions given here. But neither seem working. Should we have a separate pandas environment for this? I haven't tried it though!

Cheers

tavareshugo commented 7 months ago

I believe the mamba activate tb-profiler environment should have pandas installed.

tavareshugo commented 7 months ago

Again, I'll add a more explicit note to activate that environment first. Let's keep the issue open so I don't forget :)

avantonder commented 7 months ago

Yes, tb-profiler environment needs pandas installed. I use it when running python scripts later on

bsalehe commented 7 months ago

Eventually the script worked with seqtk env but not tb-profiler.

Cheers