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bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
105 stars 16 forks source link

Issue with pandas dependency #40

Closed jordiabante closed 1 year ago

jordiabante commented 2 years ago

Hi Matthew,

I tried installing MGEfinder on Stanford's sherlock through conda and it seemed to finish successfully. However, the help command mgefinder —help results in the following error:

ModuleNotFoundError: No module named ‘pandas.compat'

I also tried installing a more up-to-date version of pandas, but still produces the same error. I figured you might be able to help me, considering that you probably used sherlock to develop the tool. Do you know what might be going on?

Thanks!

durrantmm commented 1 year ago

Hi! I actually didn't use sherlock to develop the tool. If possible, I would use the singularity installation for batch computing. I don't really know how to help you otherwise.

abehr commented 1 year ago

In case anyone else runs into this issue, it's caused by a known anaconda issue where conda environment supersedes its own libraries with ones installed in .local instead. We were able to fix it by setting env var PYTHONNOUSERSITE.

durrantmm commented 1 year ago

Great! Thank you for explaining this.