Docker_conda_build.sh

# Command I use to build the image
# docker buildx build --build-arg CONDA_PACKAGES=./envs/nsap_packages.txt --platform linux/amd64 -t alantwaddle/nsap_test:1.6 --push .

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FROM continuumio/miniconda3

LABEL author="Alan Twaddle"
LABEL author.email="alan.twaddle@neochromosome.com"
LABEL company="neochromosome"

# This is a text file listing a package name on each line.
ARG CONDA_PACKAGES

# Check this for conda in docker
# https://pythonspeed.com/articles/activate-conda-dockerfile/

COPY ${CONDA_PACKAGES} conda_packages.txt

# mamba is a faster package manager than conda. Redundant, yes, 
# but the speed gain is > 100% when building this image
RUN conda install mamba -n base -c conda-forge
RUN conda create -n nsap

# Install packages with mamba
RUN mamba install -n nsap -y --file conda_packages.txt -c bioconda -c conda-forge

# Adding this command to the .bashrc ensures the environment is executed in a session 
RUN echo "source activate nsap" > ~/.bashrc  

# overrides the default shell to run in the conda env
SHELL ["conda", "run", "-n", "nsap", "/bin/bash", "-c"]

# Copying local python project and installing it locally
# TODO: Figure out how to do this with git.
COPY . /opt/nsap
WORKDIR /opt/nsap
RUN pip3 install -e .

# An AWS EBS storage volume is mounted here
WORKDIR /data

# This appends every command to it, again ensuring it runs in the conda env
ENTRYPOINT [ "conda", "run", "--no-capture-output", "-n", "nsap" ]