Conda+Docker for running clusterProfiler

conda_docker_clusterProfiler.txt

# The build-stage image:
FROM continuumio/miniconda3 AS build

# Install the package as normal:
COPY environment.yml ClusterProfiler_Enrichment.R /
RUN conda install -y -c conda-forge mamba && mamba env create -f environment.yml

# Install conda-pack
# Use conda-pack to create a standalone enviornment
# in /venv:
RUN mamba install -y -c conda-forge conda-pack && conda-pack -n clusterprofiler -o /tmp/env.tar && \
mkdir /venv && mv ClusterProfiler_Enrichment.R /venv && cd /venv && tar xf /tmp/env.tar && \
rm /tmp/env.tar && /venv/bin/conda-unpack && mkdir -p /data/in /data/out

# We've put venv in same path it'll be in final image,
# so now fix up paths:
#RUN /venv/bin/conda-unpack


# The runtime-stage image; we can use Debian as the
# base image since the Conda env also includes Python
# for us.
FROM debian:buster AS runtime

# Copy /venv from the previous stage:
COPY --from=build /venv /venv

# When image is run, run the code with the environment
# activated:
SHELL ["/bin/bash", "-c"]
ENV PATH=$PATH:/data/
ENTRYPOINT source /venv/bin/activate && \
Rscript /venv/ClusterProfiler_Enrichment.R
########################################

where enviroment.yml is as such:
name: clusterprofiler
channels:
- conda-forge
- bioconda
dependencies:
- conda-forge::mamba
- bioconda::bioconductor-clusterprofiler
- bioconda::bioconductor-org.hs.eg.db
- bioconda::bioconductor-org.mm.eg.db