Error: No module named 'busco' about transpi HOT 4 CLOSED

Hello,

I think the issue is in the order of your $PATH. It looks that the installation of your local busco is higher. You can remove the specific address of the local busco from $PATH. But be careful not to remove others that are essential for the system. Is the local busco under your linuxbrew installation?

Best,
Ramón

from transpi.

Hello @gabrielnsil,

Yes, it may be that TransPi is trying to use the BUSCO installed in your server but that is very odd and should not happen. Maybe your local busco is located higher in the PATH and is using that one instead of the conda env.

Can you activate the individual env of BUSCO created by TransPi and call BUSCO normally?

conda activate /home/porifera/TransPi/condaEnv/env-e8d22bfae5e32eac973114001910dada

busco -h

Let me know.

Best,
Ramón

from transpi.

Hello Ramón, thank you for the reply

Yes, I can activate the individual condaEnv of BUSCO created by TransPi but the No module named 'busco' persists. The command which busco shows the path for the BUSCO installed in my server, even with this individual condaEnv activated. I already reinstalled TransPi from scratch 3 times but the problem continues.

Curiously, with the condaEnv activated and using the which command, I observed that some tools called are from my server while others are from the condaEnv. It is normal?
Example:

which fuse-ranges
~/TransPi/condaEnv/env-e8d22bfae5e32eac973114001910dada/bin/fuse-ranges

which nhmmer
/home/linuxbrew/.linuxbrew/bin/nhmmer

I really have no more ideas on how to go from here, maybe clean up the $PATH variable prior to the execution of TransPi?

Thank you for your time,
Gabriel

from transpi.

Hello,

I think the issue is in the order of your $PATH. It looks that the installation of your local busco is higher. You can remove the specific address of the local busco from $PATH. But be careful not to remove others that are essential for the system. Is the local busco under your linuxbrew installation?

Best, Ramón

I've also encountered the same "No module named 'busco'" problem and it is indeed the result of incorrect order of environment variable. Add a command of

export PATH="/home/$USER/miniconda3/envs/BUSCO/bin"

will help to solve this problem.
Thanks for your helping!

Best,
Ryann

from transpi.