Conda activate doesn't work in bash file

I’ve installed Qiime2 2020.8 in a conda environment and followed all the steps on When I activate Qiime2 in the terminal (using conda activate qiime2-2020.8) all goes well, but when I try to run this command from within a bash file, it gives me an error message saying

CommandNotFound: Your shell has not been properly configured to use ‘conda activate’.
To initialize your shell, run
$ conda init {SHELL_NAME}

When I do this, there is no action taken, implying it should all be fine. Again, this works for activating in the shell, but not for activating in a bash file. Does anyone know how to solve this? Thanks in advance!

1 Like

Hello @aliciaocke. Try using source activate qiime2-2020.8 instead of conda activate qiime2-2020.8 in your bash script. If that doesn’t work, try add the line source ~/miniconda3/etc/profile.d/ before your conda activate. Thank you.


This worked for me, thanks! I also removed the bash extention from the file in order to make this work, in case other people also didn’t know conda activate doesn’t work in bash files.


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.