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"]

Answer 2

You can set CONDA_DEFAULT_ENV

Like this:

FROM continuumio/miniconda3

ARG conda_env=mro_env

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

ENV PATH /opt/conda/envs/$conda_env/bin:$PATH
ENV CONDA_DEFAULT_ENV $conda_env

CMD [ "python", "test.py" ]

UPDATE:

Better use activate. Work for me:

FROM continuumio/miniconda3

ADD /src/environment.yml /src/environment.yml

RUN conda env create -f /src/environment.yml
ENV PATH /opt/conda/envs/mro_env/bin:$PATH
RUN /bin/bash -c "source activate mro_env"

CMD [ "python", "test.py" ]

Answer 3

For me, the solution introduced here worked seemlessly:

FROM continuumio/miniconda3
RUN conda create -n env python=3.6
RUN echo "source activate env" > ~/.bashrc
ENV PATH /opt/conda/envs/env/bin:$PATH

Answer 4

As the user merv points out in one of the comments above (sorry don't have enough rep to vote up the comment) conda run buffers all stdout/stderr, thus making it not workable for applications interacting or even just displaying logs over I/O.

I noticed there was no accepted answer, so I just post what has worked very well for me:

You can use an entrypoint script to activate the conda enviroment and let it take over further input from the Dockerfile such that the python script can be executed within the activated conda environment

Example Dockerfile:

FROM continuumio/miniconda3

# make docker use bash instead of sh
SHELL ["/bin/bash", "--login", "-c"]

# copy all necessary files
COPY environment.yml .
COPY ownchain/mypyscript.py .
COPY entrypoint.sh /usr/local/bin/

# make entrypoint script executable
RUN chmod u+x /usr/local/bin/entrypoint.sh
# create environment
RUN conda env create -f environment.yml

ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
CMD ["python", "mypyscript.py"]

Where the entrypoint.sh looks like this:

#!/bin/bash --login
set -e

# activate conda environment and let the following process take over
conda activate myenv
exec "$@"

All credit to David R. Pugh from this post that has more details, in particular with regards to Jupyter.