first do a

conda activate bioinfor

did it work? and if so then what does the

conda list 

print?

In general, your errors look as if conda is not properly activated when the doctor.py is run

from biostar-handbook.

Hi, it says - command not found.

from biostar-handbook.

sounds like conda is not installed quite right

what happens at steps 3,4,5 in the step-by-step instructions:

https://www.biostarhandbook.com/step-by-step.html

from biostar-handbook.

Hi, @ialbert I did not notice anything out of the ordinary in those steps. They seemed to execute without a hitch.

from biostar-handbook.

So I just tried troubleshooting and I uninstalled everything and was trying again. Unfortunately the Ubuntu 22.04 version I was using before did not work at all. It said "System cannot find file". I downloaded just the app titled "Ubuntu" and I could at least get through the username steps. I also realized there's an automatic installation and the step-by-step is the manual one? While doing the automatic one its stopped with the following errors. Please let me know if this tells you anything and what I could try? @ialbert

7/10 Installing bioinformatics software

Traceback (most recent call last):
File "/home/bstarnush/miniconda3/condabin/mamba", line 7, in
from mamba.mamba import main
File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 49, in
import libmambapy as api
File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/libmambapy/init.py", line 7, in
raise e
File "/home/bstarnush/miniconda3/lib/python3.10/site-packages/libmambapy/init.py", line 4, in
from libmambapy.bindings import * # noqa: F401,F403
ImportError: libarchive.so.13: cannot open shared object file: No such file or directory

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Was able to figure out that my bioinfo environment was not activated.

from biostar-handbook.