Use GitHub Actions (#9)

* Create build-container.yml

* Update build-container.yml

* Update build-container.yml

* Update a yml for GitHub Actions

* Update build-container.yml

* Update Dockerfile

* Update cyrest.version

* Update Dockerfile

* Create docker-compose.yml

* Remove Dockerfiles for py4cy and RCy3

* Update docker-compose.yml

* Add fluxbox to Cytoscape Desktop env

* Use .env file to set PORT number or SCREEN size

* Update build-container.yml

.env

@@ -0,0 +1,8 @@
+NOVNC_PORT=6080
+NOVNC_SCREEN_WIDTH=1920
+NOVNC_SCREEN_HEIGHT=1080
+CYREST_PORT=1234
+
+JUPYTER_PORT=8888
+JUPYTER_TOKEN=token
+JUPYTER_PASSWORD=password

.github/workflows/build-container.yml

@@ -0,0 +1,43 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Publish Docker image
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: cytoscape/cytoscape-desktop
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

base/Dockerfile → Dockerfile

@@ -1,24 +1,26 @@
-FROM ubuntu:20.04
+FROM ubuntu:22.04
 
 # PARAMETERS
-ENV CYTOSCAPE_VERSION 3.9.1
+ENV CYTOSCAPE_VERSION 3.10.1
+ENV TZ=Asia/Tokyo
 
 # CHANGE USER
 USER root
 
 # INSTALL JAVA
-RUN apt-get update && apt-get -y install default-jdk libxcursor1 xvfb supervisor wget x11vnc novnc websockify
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+RUN apt-get update && apt-get -y install openjdk-17-jdk libxcursor1 xvfb supervisor wget x11vnc novnc websockify fluxbox
 RUN wget https://github.com/cytoscape/cytoscape/releases/download/${CYTOSCAPE_VERSION}/cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
 RUN tar xf cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz && rm cytoscape-unix-${CYTOSCAPE_VERSION}.tar.gz
 RUN cd /cytoscape-unix-${CYTOSCAPE_VERSION}/framework/system/org/cytoscape/property-impl/${CYTOSCAPE_VERSION} \
     && jar -xf property-impl-${CYTOSCAPE_VERSION}.jar cytoscape3.props \
-    && cat cytoscape3.props | sed "s/^cyrest.version.*/cyrest.version=3.12.3/g" > cytoscape3.props.tmp \
+    && cat cytoscape3.props | sed "s/^cyrest.version.*/cyrest.version=3.13.2/g" > cytoscape3.props.tmp \
     && mv cytoscape3.props.tmp cytoscape3.props \
     && jar -uf property-impl-${CYTOSCAPE_VERSION}.jar cytoscape3.props \
     && rm cytoscape3.props \
     && cd /
 # Set JAVA_HOME From sudo update-alternatives --config java
-RUN echo 'JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64"' >> /etc/environment
+RUN echo 'JAVA_HOME="/usr/lib/jvm/java-17-openjdk-amd64"' >> /etc/environment
 
 COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
 CMD ["/usr/bin/supervisord"]

compose.yml

@@ -0,0 +1,20 @@
+version: '3.10.1'
+services:
+
+  cytoscape-desktop:
+    image: cytoscape/cytoscape-desktop:3.10.1
+    ports:
+      - '${NOVNC_PORT}:${NOVNC_PORT}'
+    environment:
+      - XVFB_SCREEN_WIDTH=${NOVNC_SCREEN_WIDTH}
+      - XVFB_SCREEN_HEIGHT=${NOVNC_SCREEN_HEIGHT}
+      - NOVNC_PORT=${NOVNC_PORT}
+      - CYREST_PORT=${CYREST_PORT}
+
+  jupyter:
+    image: jupyter/datascience-notebook
+    ports:
+      - '${JUPYTER_PORT}:${JUPYTER_PORT}'
+    environment:
+      - JUPYTER_TOKEN=${JUPYTER_TOKEN}
+      - PASSWORD=${JUPYTER_PASSWORD}

supervisord.conf

@@ -0,0 +1,40 @@
+[supervisord]
+nodaemon=true
+
+[program:xvfb]
+priority=1
+directory=/
+command=/usr/bin/Xvfb :1 -screen 0 "%(ENV_XVFB_SCREEN_WIDTH)s"x"%(ENV_XVFB_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:x11vnc]
+command=/bin/bash -c 'x11vnc -forever -shared -display :1 -auth /root/.Xauth'
+priority=11
+
+[program:fluxbox]
+priority=20
+directory=/root
+command=/usr/bin/fluxbox -rc /etc/fluxbox_init
+user=root
+autostart=true
+autorestart=true
+stopsignal=TERM
+environment=DISPLAY=":1",HOME="/root"
+stdout_logfile=/var/log/fluxbox.log
+stderr_logfile=/var/log/fluxbox.err
+
+[program:chrome]
+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"
+
+[program:novnc]
+command=/bin/bash -c 'websockify -D --web=/usr/share/novnc/ %(ENV_NOVNC_PORT)s localhost:5900'