Ambertools not found by BioSimSpace in jupyterlab

[kexul]

I just tried https://try.openbiosim.org/ with the quick start guide here: https://biosimspace.openbiosim.org/quickstart/index.html .
An error occurred:

!mamba install ambertools -c conda-forge says ambertools has already been installed.
I tried os.environ['AMBERHOME'] = /opt/conda, but it doesn't help either.

[chryswoods]

Interesting... I've just tried and I get the same result. But - if I run this via ipython in the Jupyter lab Terminal, then everything works. The AMBERHOME environment variable is correctly set. But, it isn't set in the notebook.

Somehow, AMBERHOME is set in a shell in the Terminal, but not in the notebook.

Looking into this, I see that Jupyter now doesn't spawn a shell for the notebook, and so ignores the environment variables set in the bashrc file. The way to initialise variables is to put them into a startup script in $HOME/.ipython/profile_default/startup/00-env.py, e.g.

import os

os.environ["AMBERHOME"] = "/opt/conda"

I've done this for a temporary session, and it work. I will now update the notebook container image to do this generally. Everything should be ready in about 10-20 minutes (or so).

[lohedges]

Ah, interesting. This might explain some of the issues that I was seeing with GROMACS/PLUMED too, i.e. it worked on the command-line but not in the notebook. (The first time I tried it anyway.)

[chryswoods]

All fixed now. I ended up putting the environment variables into the docker image. I also added PLUMED_ROOT which I had missed before. I think everything should be working now (I've just tested myself, and it is good :-))