largely functional dockerfile

containers/docker/Dockerfile

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+FROM mambaorg/micromamba
+
+WORKDIR /home/$MAMBA_USER
+
+# root level stuff
+USER root
+RUN apt-get update
+RUN apt-get install -y git
+
+RUN mkdir /home/data
+RUN chown $MAMBA_USER /home/data
+
+USER $MAMBA_USER
+
+# get source code
+RUN git clone https://github.com/medema-group/BiG-SCAPE.git -b feature/repo-updates
+
+WORKDIR /home/$MAMBA_USER/BiG-SCAPE
+
+# set up environment
+RUN micromamba install \
+    # channel
+    -c conda-forge \
+    # accept all prompts
+    -y \
+    # name of env
+    -n base \
+    # get python
+    -f environment.yml && \
+    # clean up cache
+    micromamba clean --all --yes
+
+RUN chmod u+x bigscape.py
+
+ENTRYPOINT [ "/usr/local/bin/_entrypoint.sh", "./bigscape.py" ]
+CMD [ "--help" ]