Adding a Dockerfile for our noVNC images

fiji-novnc-rocky/Dockerfile

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+
+#
+# Fiji + Java 8 Dockerfile
+#
+
+
+# Use Rocky 9.2-based RIS THPC image as base
+FROM ghcr.io/washu-it-ris/novnc:rocky9.2
+
+
+# Define maintainer.
+LABEL maintainer="japrewit@wustl.edu"
+LABEL org.opencontainers.image.source="https://github.com/WashU-IT-RIS/fiji-dockerfiles"
+
+# Install OpenJDK 8 for Fiji
+USER root
+RUN dnf install -y java-1.8.0-openjdk-devel unzip wget \
+	&& dnf clean all
+
+
+RUN useradd -u 1000 -ms /bin/bash fiji \
+	&& mkdir -p /opt/fiji \
+	&& chown -R fiji:fiji /opt/fiji
+
+
+COPY entrypoint.sh /opt/fiji
+RUN chown fiji:fiji /opt/fiji/entrypoint.sh \
+	&& chmod 755 /opt/fiji/entrypoint.sh
+
+
+# Set HOME for the fiji user
+ENV HOME /opt/fiji
+USER fiji
+
+
+# Define working directory.
+WORKDIR /opt/fiji
+
+# Install Fiji.
+RUN wget -q https://downloads.imagej.net/fiji/stable/fiji-stable-linux64-jdk.zip \
+ && unzip fiji-stable-linux64-jdk.zip  \
+ && rm fiji-stable-linux64-jdk.zip 
+
+# Add fiji to the PATH
+ENV PATH $PATH:/opt/fiji/Fiji.app
+
+
+# Define entrypoint.
+ENTRYPOINT ["./entrypoint.sh"]
+
+# Update URLs use https
+RUN ./entrypoint.sh --update edit-update-site ImageJ https://update.imagej.net/
+RUN ./entrypoint.sh --update edit-update-site Fiji https://update.fiji.sc/
+RUN ./entrypoint.sh --update edit-update-site Java-8 https://sites.imagej.net/Java-8/
+
+# Run once to create Java preferences.
+COPY --chown=fiji:fiji demo.py /opt/fiji/
+RUN ./entrypoint.sh --headless --ij2 --console --run ./demo.py 'name="test"'

fiji-novnc-rocky/demo.py

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+#@String name
+print('Hello ' + name)

fiji-novnc-rocky/entrypoint.sh

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+#!/bin/bash
+#
+# Entrypoint for the docker image which tries to do
+# the most sensible thing for the user:
+#
+#   (A) If no arguments are passed, print help:
+#   $ docker run fiji
+#
+#   (B) If no arguments are passed but a ternimal is requested, open a shell:
+#   $ docker run -ti fiji
+#
+#   (C) Otherwise, assume arguments are to be passed to ImageJ-linux64:
+#   $ docker run fiji --console --run /my/script.py
+#
+#   (D) Unless, the command starts with an executable, in which case run it:
+#   $ docker run fiji ImageJ-linux64 --console --run /my/script.py
+
+# Command run by default
+IMAGEJ=${IMAGEJ:-"ImageJ-linux64 --headless --default-gc"}
+
+# For debugging purposes
+RUN=${RUN:-exec}
+
+set -e
+
+if [[ $# -eq 0 ]] ; then
+    if [ -t 0 ] ; then
+        # (B) start a shell
+        $RUN bash
+    else
+        # (A) print help and exit
+        $RUN $IMAGEJ --help
+    fi
+else
+    COMMAND=$1
+    if command -v "$COMMAND" >/dev/null 2>&1; then
+        # (D) if the user has passed e.g. ImageJ-linux64,
+        # then run it verbatim for backwards compatibility
+        $RUN "$@"
+    else
+        # (C) Expected usage
+        $RUN $IMAGEJ "$@"
+    fi
+fi