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NAL-i5K / GFF3toolkit

Python programs for processing GFF3 files
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No module named 'gff3tool' #138

Closed emilpaulitz closed 3 months ago

emilpaulitz commented 4 months ago

Hi team,

I want to merge multiple gff files using gff3_merge. However, I have trouble with the install as described in the github Readme. I create a fresh environment with the stated prerequisites python and perl (python is installed with version 3.12.4, wheel is also installed), and then install gff3tool with pip:

mamba create -n gff3tools python perl
pip install gff3tool

However, when I call gff3_merge with any or no arguments, I immediately receive the error 

Traceback (most recent call last):
  File "~/.local/bin/gff3_merge", line 6, in <module>
    from gff3tool.bin.gff3_merge import script_main
ModuleNotFoundError: No module named 'gff3tool'

Any ideas what could be the issue?

emilpaulitz commented 3 months ago

Solved it. My mamba version is installed locally, while conda is managed server-wide. Somehow the mamba environment did not work for gff3_tools. Calling conda deactivate until nothing changed anymore, and reinstalling everything with conda instead of mamba worked. Probably a very specific situation.

mpoelchau commented 3 months ago

I'm glad you figured that out @emilpaulitz! Thanks for the update.

I'm going to close the issue, but feel free to reopen it if anything related pops up.