Problems running conda update in a dockerfile

Question

I am trying to create a docker container with some conda environments. When I run the container in interactive mode running

conda update --all
conda env create -f env.yml

runs with no issues. However whenever I try to execute these commands with a Docker file I recieve

/bin/sh: 1: conda: command not foud

Docker file is shown below:

FROM ubuntu:latest
RUN apt-get update && \
    apt-get install unzip && \
    mkdir /install && \
    apt-get install nano
COPY Anaconda3-2018.12-Linux-x86_64.sh env.yml /install/
WORKDIR /install
RUN bash Anaconda3-2018.12-Linux-x86_64.sh -b && \
    echo "export PATH="/root/anaconda3/bin:$PATH"" >> ~/.bashrc && \
    /bin/bash -c "source ~/.bashrc"
RUN conda update --all
RUN conda env create -f env.yml

So it appears that sh is being used instead of bash so I edited the Dockerfile to the following:

FROM ubuntu:latest
RUN apt-get update && \
    apt-get install unzip && \
    mkdir /install && \
    apt-get install nano
COPY Anaconda3-2018.12-Linux-x86_64.sh env.yml /install/
WORKDIR /install
RUN bash Anaconda3-2018.12-Linux-x86_64.sh -b && \
    echo "export PATH="/root/anaconda3/bin:$PATH"" >> ~/.bashrc && \
    /bin/bash -c "source ~/.bashrc"
RUN /bin/bash -c "conda update --all"

with the following error

/bin/bash: conda: command not found

Answer 1

You have to add anaconda to the PATH during build time with the ENV variable before executing anaconda inside the Dockerfile.

RUN bash Anaconda3-2018.12-Linux-x86_64.sh -b && \
    echo "export PATH="/root/anaconda3/bin:$PATH"" >> ~/.bashrc && \
    /bin/bash -c "source ~/.bashrc"
ENV PATH /root/anaconda3/bin:$PATH
RUN conda update --all

Updating PATH in .bashrc will make it possible to call conda inside the container, when run with docker run, but not in other RUN statements in the docker file.