Dockerfile

FROM continuumio/miniconda3@sha256:a2e6aa4cd0b6dd696ae9e3e5732943250a977ab3a42b2fe5fb7ef0c19d2d9f16
LABEL description="Dockerfile containing all the requirements for the report of - " \
      author="your_email@website.domain"

ARG ENV_NAME="base"

RUN apk add --no-cache bash=5.0.17-r0 procps=3.3.16-r0 libxt-dev=1.2.0-r0

COPY environment.yml /
RUN conda env update -n ${ENV_NAME} -f environment.yml && conda clean -a

# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/${ENV_NAME}/bin:$PATH

# Dump the details of the installed packages to a file for posterity
RUN conda env export --name ${ENV_NAME} > ${ENV_NAME}_exported.yml

# Initialise bash for conda
RUN conda init bash

# Copy additional scripts
## bin/report/ files will be flatly copied into bin/ (no report folder)
RUN mkdir /opt/bin/
COPY bin/* /opt/bin/
RUN chmod +x /opt/bin/*
ENV PATH="$PATH:/opt/bin/"