Dockerfile

FROM continuumio/miniconda3:4.9.2-alpine
LABEL version="2.1.2" \
      description="Docker image for Pangolin"

# Install git for pangolin
RUN apk update && \
    apk add git bash

COPY environment.yml /environment.yml
# Python 3.8.5 already installed along with recent version of pip
# so remove Python and pip deps from environment.yml before installation
RUN sed -i "$(grep -n 'python>=3.7' /environment.yml | cut -f1 -d:)d" /environment.yml && \
    sed -i "$(grep -n 'pip=' /environment.yml | cut -f1 -d:)d" /environment.yml
# Install the conda environment
RUN conda env create --quiet -f /environment.yml && conda clean -a
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/pangolin/bin:$PATH

# Install Pangolin
COPY . /pangolin/
WORKDIR /pangolin/
RUN pip install . && rm -rf /root/.cache/pip
RUN pangolin --version &> /pangolin-version.txt

# Dump the details of the installed packages to a file for posterity
RUN conda env export --name pangolin > /pangolin.yml
WORKDIR /tmp/