Activating another micromamba environment upon entry

[calvinp0]

Hey. So in our docker image with micromamba as the base image, we use the command

ARG MAMBA_DOCKERFILE_ACTIVATE=1
ENV ENV_NAME=rmg_env

And then after that, in our build we also install a couple more micromamba environments.

The docker builds perfectly but upon interaction it starts with the environment as rmg_env (which is to be expected). However, we want it so that upon entry of user, they will start off with one of the other installed environments. More specifically, t3_env.

Is it possible to do this?

[maresb]

Have you tried something like this?

docker run --rm -it -e ENV_NAME=te_env your-docker-image

[wholtz]

If you want an environment automatically activated on docker run ..., without passing -e ENV_NAME=t3_env as @maresb suggested, you'll have to name that environment base.

[npow]

I have similar use-case. I'm currently activating the default base environment via the entrypoint, but then the first thing it does is sets up another conda environment dynamically. How can I switch to that conda environment after it's setup? I keep getting 'micromamba' is running as a subprocess and can't modify the parent shell. when I try to do micromamba activate <ENV_NAME>.

For example, I want to do something like the following in my entrypoint:

python trampoline.py <-- sets up <ENV_NAME>
micromamba activate <ENV_NAME>
python server.py

[wholtz]

Does this do what you need?

python trampoline.py <-- sets up <ENV_NAME>
micromamba run -n <ENV_NAME> python server.py

[maresb]

Alternatively,

source _activate_current_env.sh
python trampoline.py <-- sets up <ENV_NAME>
micromamba activate <ENV_NAME>
python server.py

The command source _activate_current_env.sh modifies your shell so that micromamba runs as a Bash function rather than the /usr/local/bin/micromamba executable. In order to be able to activate an environment in your current shell, micromamba needs to be running a Bash function.

In contrast, the micromamba run command is for one-off commands without shell activation.