How to activate a conda environment before running Docker commands

Question

I'm creating a docker image with, inside, a conda environment myEnv using a Dockerfile.

I would like, when running the docker image with

docker run -it myDockerImage

to get to a bash terminal with the environment already activated. I know we can pass variables and commands to docker run but I would like it to be done automatically.

I tried adding the following variants to the end of the Dockerfile but nothing seems to work:

CMD ["source /root/miniconda/bin/activate myEnv"]
CMD [".", "/root/miniconda/bin/activate", "myEnv"]
CMD ["source /root/miniconda/bin/activate myEnv; /bin/bash"]

Answer 1

Do this with an ENTRYPOINT in your Dockerfile.

src/entrypoint.sh

#!/bin/bash

# enable conda for this shell
. /opt/conda/etc/profile.d/conda.sh

# activate the environment
conda activate my_environment

# exec the cmd/command in this process, making it pid 1
exec "$@"

src/Dockerfile

# ...
COPY ./entrypoint.sh ./entrypoint.sh
RUN chmod +x ./entrypoint.sh
ENTRYPOINT ["./entrypoint.sh"]