Cytoscape Docker image, profiling

cytoscape_docker/Dockerfile

@@ -0,0 +1,37 @@
+# based on official Cytoscape image: https://github.com/cytoscape/docker-cytoscape-desktop
+# version more compact due to:
+# - removed unnecessary packages and instructions --> remote display not used
+# - included all environment variables within this Dockerfile, no need to use Docker compose for the build process
+FROM ubuntu:22.04
+
+# environment variables
+ENV CYTOSCAPE_VERSION=3.10.2
+ENV VIRTUAL_SCREEN_WIDTH=1920
+ENV VIRTUAL_SCREEN_HEIGHT=1080
+ENV CYREST_PORT=1234
+ENV SUPERVISOR_CFG="/etc/supervisor/conf.d/supervisord.conf"
+
+# labels
+LABEL cytoscape_version="${CYTOSCAPE_VERSION}"
+LABEL context="independent CyREST instance for graph rendering"
+
+# change user
+USER root
+# install necessary packages
+RUN apt update && apt full-upgrade -y && apt -y install \
+    libxcursor1 \
+    openjdk-17-jre \
+    supervisor \
+    wget \
+    xvfb
+# set Java home directory as permanently set ENV var
+RUN echo "export JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64" >> /root/.bashrc
+# download and extract Cytoscape
+RUN wget https://github.com/cytoscape/cytoscape/releases/download/${CYTOSCAPE_VERSION}/cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
+RUN tar -xf cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz && rm cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
+
+# supervisord config
+# supervisor used to start the virtual display via Xvfb and the Cytoscape process with web server (CyREST)
+COPY supervisord.conf ${SUPERVISOR_CFG}
+EXPOSE ${CYREST_PORT}
+CMD ["/usr/bin/supervisord", "-c", "/etc/supervisor/conf.d/supervisord.conf"]

cytoscape_docker/supervisord.conf

@@ -0,0 +1,22 @@
+# based on official Cytoscape image: https://github.com/cytoscape/docker-cytoscape-desktop
+[supervisord]
+nodaemon=true
+
+[program:xvfb]
+priority=1
+directory=/
+command=/usr/bin/Xvfb :1 -screen 0 "%(ENV_VIRTUAL_SCREEN_WIDTH)s"x"%(ENV_VIRTUAL_SCREEN_HEIGHT)s"x24 +extension RANDR
+user=root
+autostart=true
+autorestart=true
+stopsignal=QUIT
+stdout_logfile=/var/log/xvfb.log
+stderr_logfile=/var/log/xvfb.err
+
+[program:cytoscape]
+priority=30
+command=/bin/bash -c 'rm -rf /root/CytoscapeConfiguration && /cytoscape-unix-%(ENV_CYTOSCAPE_VERSION)s/cytoscape.sh --rest %(ENV_CYREST_PORT)s'
+user=root
+autostart=true
+stopsignal=QUIT
+environment=DISPLAY=":1",HOME="/root"