Dockerfile for Ubuntu-based Bioconda environment on Apple Silicon (M1/M2/M3/M4) architecture

Dockerfile

FROM --platform=linux/amd64 ubuntu:24.10 AS bioinf
# --platform specification here is crucial because as of now,
# without specifying it Docker starts building for ARM 
# by default, which leads to "rosetta: failed to open elf" errors.

RUN apt-get update && apt-get install -y less vim wget
# Install other utilities of your liking. Specifically, if git is needed:
# RUN apt-get install git && mkdir -p /root/.ssh && ssh-keyscan github.com >> /root/.ssh/known_hosts
# ssh-keyscan is invoked for git clone to work. Note that only GitHub will work now, change to required host.

# Installing miniconda

RUN mkdir -p /miniconda3
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /miniconda3/miniconda.sh
RUN bash /miniconda3/miniconda.sh -b -u -p /miniconda3 && rm /miniconda3/miniconda.sh
RUN bash -c "source /miniconda3/bin/activate && conda init --all"
# All conda commands in the dockerfile should start with "bash -c "source ..."" 
# part for Docker to see conda binary.

# Installing mamba

RUN bash -c "source /miniconda3/bin/activate &&  \
    conda install -y conda-forge::mamba"

# Installing bioconda

RUN bash -c "source /miniconda3/bin/activate &&  \
    conda config --add channels bioconda && \
    conda config --add channels conda-forge && \
    conda config --set channel_priority strict"

# Installing required tools

RUN bash -c "source /miniconda3/bin/activate &&  \
    mamba install -y bedtools samtools star"
# These tools are installed into the default conda env.
    
RUN bash -c "source /miniconda3/bin/activate &&  \
    mamba create -y --name cufflinks-env cufflinks"
# This tool is installed into its own conda env.
# (In this particular example, cufflinks requires
# too old version of Python to be compatible with
# other packages.)

VOLUME ["/data"]
WORKDIR /data
CMD ["bash"]

# Build:
#    docker build -t bioinf --target bioinf .
# Run:
#    docker run -it -v .:/data bioinf