--- name: docker-image-deployment description: Use when when you have a containerized scientific tool available on Docker Hub (e. license: CC-BY-4.0 metadata: edam_operation: http://edamontology.org/operation_3763 edam_topics: - http://edamontology.org/topic_3173 - http://edamontology.org/topic_0625 tools: - Docker - MetFrag - Tomcat - Java 21 techniques: - mass-spectrometry derived_from: - doi: 10.1186/s13321-016-0115-9 title: MetFrag evidence_spans: - docker run -it --rm -p 8888:8080 ipbhalle/metfragweb - This container packages the MetFrag (https://github.com/ipb-halle/MetFragRelaunched) webapp claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_metfrag_cq doi: 10.1186/s13321-016-0115-9 title: MetFrag dedup_kept_from: coll_metfrag_cq schema_version: 0.2.0 attribution: generator: AgenticScienceBuilder original_doi: 10.1186/s13321-016-0115-9 all_source_dois: - 10.1186/s13321-016-0115-9 zenodo_doi: 10.5281/zenodo.20794027 curators: [] promoter: Louis-Félix Nothias sponsor: CNRS & Université Côte d'Azur --- # docker-image-deployment ## Summary Deploy a containerized scientific application (MetFrag webapp) by pulling a Docker image, mapping network ports, configuring runtime environment variables, and verifying HTTP accessibility at the exposed endpoint. This skill bridges container orchestration with application deployment validation. ## When to use When you have a containerized scientific tool available on Docker Hub (e.g., ipbhalle/metfragweb) and need to make it accessible on a host at a specified HTTP endpoint, or when you need to customize JVM memory, web application paths, or configuration files at container runtime without rebuilding the image. ## When NOT to use - The containerized application requires persistent data storage across container restarts and you have not set up a named volume or bind mount for the application state. - You need to run multiple instances with coordinated networking or service discovery; use Docker Compose or Kubernetes instead of single docker run commands. - The host system does not have Docker installed or you lack permission to run privileged Docker commands. ## Inputs - Docker image name and tag (string, e.g., 'ipbhalle/metfragweb') - Host port number (integer) - Container internal port number (integer, typically 8080 for Tomcat) - Optional: JVM memory configuration string (e.g., '-Xmx4g -Xms4g') - Optional: WEBPREFIX string (e.g., 'mymetfrag') - Optional: settings.properties file (path on host filesystem) ## Outputs - Running Docker container instance accessible at HOST:HOST_PORT - HTTP endpoint responding with application homepage (HTTP 200) - Container startup logs documenting Tomcat initialization - Deployed MetFrag webapp accessible via web browser or HTTP client ## How to apply Pull the Docker image from the registry (e.g., docker pull ipbhalle/metfragweb). Run the container using docker run with port mapping (-p HOST_PORT:CONTAINER_PORT, typically -p 8888:8080 for Tomcat). Set environment variables (JAVA_OPTS for JVM memory heap sizes, WEBPREFIX for the webapp path, or settings.properties file location) as needed. Mount configuration files via -v HOST_PATH:/resources/settings.properties if using custom settings. Allow time for the embedded Tomcat application server to initialize. Verify successful deployment by making a GET request to the exposed HTTP endpoint (e.g., http://localhost:8888/MetFragWeb) and confirming a 200 response or valid webpage content is returned. ## Related tools - **Docker** (Container runtime and orchestration—pulls, runs, and manages the containerized MetFrag webapp with port mapping and environment variable configuration.) - **Tomcat** (Embedded Java web application server inside the container—listens on internal port 8080 and serves the MetFrag webapp after initialization.) - **Java 21** (Runtime environment required by MetFrag; JVM memory heap sizes are configured via JAVA_OPTS environment variable.) - **MetFrag** (Scientific application packaged in the Docker image; provides mass spectrometry analysis web interface.) — https://github.com/ipb-halle/MetFragRelaunched ## Examples ``` docker run -it --rm -e JAVA_OPTS="-Xmx4g -Xms4g" -e WEBPREFIX=mymetfrag -v $(pwd)/settings.properties:/resources/settings.properties -p 8888:8080 ipbhalle/metfragweb ``` ## Evaluation signals - HTTP GET request to http://localhost:HOST_PORT/WEBPREFIX returns HTTP status 200 and valid HTML content. - Container logs show successful Tomcat startup messages with no ERROR or FATAL level entries during initialization. - Port mapping is active: `docker ps` shows the container with PORTS column displaying `0.0.0.0:HOST_PORT->8080/tcp`. - Custom environment variables are applied: if JAVA_OPTS is set, the JVM process inside the container reports the configured heap sizes via `jps -v` or container logs. - Configuration file is mounted correctly: if settings.properties is provided via -v, the running container's /resources/settings.properties is readable and contains expected configuration parameters (e.g., ChemSpiderToken, proxy settings). ## Limitations - The container requires the Docker daemon to be running and accessible; deployment will fail on systems without Docker or with permission restrictions. - JVM memory limits (JAVA_OPTS) must be less than the host system's total available memory; misconfiguration causes out-of-memory container termination. - Port 8080 inside the container is hardcoded; if you need the webapp on a different internal port, you must rebuild the image or use a reverse proxy. - Configuration via settings.properties is not validated at container startup; invalid proxy or database credentials will only be detected when those services are first queried at runtime. - No automatic health checks or restart policies are configured by default; the container will exit if Tomcat crashes, and manual intervention is required to restart. ## Evidence - [readme] This container packages the MetFrag (https://github.com/ipb-halle/MetFragRelaunched) webapp and some text databases based on the latest official tomcat docker container.: "This container packages the MetFrag (https://github.com/ipb-halle/MetFragRelaunched) webapp and some text databases based on the latest official tomcat docker container." - [readme] Run MetFrag at http://localhost:8888/MetFragWeb docker run -it --rm -p 8888:8080 ipbhalle/metfragweb: "docker run -it --rm -p 8888:8080 ipbhalle/metfragweb" - [readme] environment variable JAVA_OPTS="-Xmx?g -Xms?g" to adjust jvm memory: "environment variable JAVA_OPTS="-Xmx?g -Xms?g" to adjust jvm memory" - [readme] Run Metfrag at http://localhost:8888/mymetfrag with 4GB JVM size using a settings file from ./settings.properties docker run -it --rm -e JAVA_OPTS="-Xmx4g -Xms4g" -e WEBPREFIX=mymetfrag -v $(pwd)/settings.properties:/resources/settings.properties -p 8888:8080 ipbhalle/metfragweb: "docker run -it --rm -e JAVA_OPTS="-Xmx4g -Xms4g" -e WEBPREFIX=mymetfrag -v $(pwd)/settings.properties:/resources/settings.properties -p 8888:8080 ipbhalle/metfragweb" - [other] The MetFrag webapp is deployed by running the ipbhalle/metfragweb Docker container with port mapping (-p 8888:8080) to expose the internal Tomcat port 8080 to the host port 8888, making the application accessible at the specified HTTP endpoint.: "The MetFrag webapp is deployed by running the ipbhalle/metfragweb Docker container with port mapping (-p 8888:8080) to expose the internal Tomcat port 8080 to the host port 8888" - [readme] automatic use of a metfrag settings file if provided at /resources/settings.properties: "automatic use of a metfrag settings file if provided at /resources/settings.properties"