python - Activate conda environment in docker

Question

I need to activate environment in docker and run a command in this environment. I create the environment, but then I try to activate this environment and run the command in this way:

CMD [ "source activate mro_env && ipython kernel install --user --name=mro_env" ]

but when I ran docker I get an error:

[FATAL tini (8)] exec source activate mro_env && ipython kernel install 
--user --name=mro_env failed: No such file or directory

This is the whole Dockerfile:

FROM continuumio/miniconda3

ADD /src/mro_env.yml /src/mro_env.yml
RUN conda env create -f /src/mro_env.yml

# Pull the environment name out of the mro_env.yml
RUN echo "source activate $(head -1 /src/mro_env.yml | cut -d' ' -f2)" > ~/.bashrc
ENV PATH /opt/conda/envs/$(head -1 /src/mro_env.yml | cut -d' ' -f2)/bin:$PATH

CMD [ "source activate mro_env && ipython kernel install --user --name=mro_env" ]

Answer 1

Followed this tutorial and it worked. Example Dockerfile:

FROM continuumio/miniconda
WORKDIR /usr/src/app
COPY ./ ./
RUN conda env create -f environment.yml

# Make RUN commands use the new environment:
SHELL ["conda", "run", "-n", "myenv", "/bin/bash", "-c"]

EXPOSE 5003
# The code to run when container is started:
ENTRYPOINT ["conda", "run", "-n", "myenv", "python3", "src/server.py"]

Update:

You can use "conda run --no-capture-output" to not buffer IO if you use the 4.9 version of conda. Updated Dockerfile:

FROM continuumio/miniconda
WORKDIR /usr/src/app
COPY ./ ./
RUN conda env create -f environment.yml

# Make RUN commands use the new environment:
SHELL ["conda", "run", "--no-capture-output", "-n", "myenv", "/bin/bash", "-c"]

EXPOSE 5003
# The code to run when container is started:
ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "myenv", "python3", "src/server.py"]