Create Dockerfile

Dockerfile

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+# A modified verion of Corey's Dockerfile from: https://github.com/CorwinAnsley/artifice/blob/main/artifice/docker_rampart/Dockerfile
+# This will create a docker container that can run rampart and comes preloaded with the mpvx rampart protocol
+
+RUN apt install build-essential -y --no-install-recommends
+
+# copy in protocol files
+RUN git clone https://github.com/artic-network/rampart-mpxv
+
+# install rampart
+# This is a fork of rampart with "nodejs" pinned to 20.7.0
+# Using the original rampart environment.yml leads to an npm version issue.
+RUN git clone https://github.com/artic-network/rampart.git
+
+# create rampart environment
+RUN conda env create -f /data/rampart/environment.yml
+
+# Install conda-pack:
+RUN conda install -c conda-forge conda-pack
+
+# Use conda-pack to create a standalone enviornment
+# in /venv:
+RUN conda-pack -n artic-rampart -o /tmp/env.tar && \
+  mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
+  rm /tmp/env.tar
+
+# We've put venv in same path it'll be in final image,
+# so now fix up paths:
+RUN /venv/bin/conda-unpack
+
+#removing git files and example data to save space in final image
+RUN rm -rf /data/rampart/.git && rm -rf /data/rampart/example_data
+
+SHELL ["/bin/bash", "-c"]
+
+WORKDIR /data/rampart
+
+# update npm, install npm packages, build rampart
+RUN export NODE_OPTIONS=--openssl-legacy-provider && \
+    source /venv/bin/activate && npm install  && \
+    npm run build && npm install --global .
+
+# runtime image
+FROM debian:buster-slim AS runtime-image
+
+COPY --from=compile-image /data/rampart /data/rampart
+COPY --from=compile-image /data/rampart-mpxv /data/rampart-mpxv
+
+# Copy /venv from the previous stage:
+COPY --from=compile-image /venv /venv
+
+WORKDIR /data/run_data/
+
+# set environment variable PYTHONUNBUFFERED to allow unbuffered log output for artifice
+ENV PYTHONUNBUFFERED=1
+
+# create directories to mount the basecalled directory and protocol
+RUN mkdir -p /data/run_data/basecalled && \
+mkdir -p /data/run_data/protocol && \
+cp -a /data/rampart/default_protocol/.  /data/run_data/protocol
+
+SHELL ["/bin/bash", "-c"]
+
+# run rampart
+ENTRYPOINT source /venv/bin/activate && if ["$BARCODES" == ""] ; \
+then rampart --protocol /data/run_data/protocol --ports ${PORT_ONE} ${PORT_TWO} --basecalledPath /data/run_data/basecalled  --clearAnnotated; \
+else rampart --protocol /data/run_data/protocol --ports ${PORT_ONE} ${PORT_TWO} --basecalledPath /data/run_data/basecalled --barcodeNames ${BARCODES} --clearAnnotated ; fi