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This page provides an overview of approaches to deploy RDepot.
It is recommended to have a look at the Architecture page first to familiarize yourself with the RDepot components and their role.
OpenAnalytics-maintained docker images are available on docker hub:
The images are based on adoptopenjdk images.
Both RDepot images are available under several tagging strategies:
- versioned (e.g.
1.4.2): Recommended for production.
- snapshots (e.g.
1.5.0-SNAPSHOT): Bleeding edge. Not recommended for production.
latest: Most recent build. Not recommended for production.
Example (Docker Compose)
The following prerequisites are needed:
While not a strict requirement, docker-compose will help you better manage the multiple containers that are involved. This guide will continue to use docker-compose, but you should be able to convert the example to standard docker.
(Install i.e. by issuing
pip install docker-compose)
port 80 is not used (localhost, check for nginx or apache service)
An example docker-compose YAML file:
version: '3' services: proxy: image: library/nginx:alpine container_name: oa-rdepot-proxy restart: unless-stopped volumes: - ./docker/proxy/nginx.conf:/etc/nginx/nginx.conf:ro - ./docker/proxy/sites-enabled/rdepot:/etc/nginx/sites-enabled/rdepot:ro - repository:/opt/rdepot/repo/:ro - logs:/var/log/nginx/ ports: - 80:80 depends_on: - app - repo networks: - oa-rdepot db: image: library/postgres:alpine restart: unless-stopped hostname: oa-rdepot-db container_name: oa-rdepot-db volumes: - ./docker/db/populate_database.sh:/docker-entrypoint-initdb.d/populate_database.sh:ro - ./docker/db/rdepot.sql:/opt/rdepot.sql:ro environment: - POSTGRES_DB=rdepot - POSTGRES_USER=rdepot - POSTGRES_PASSWORD=mysecretpassword networks: - oa-rdepot app: image: openanalytics/rdepot-app:1.4.2 restart: unless-stopped hostname: oa-rdepot-app container_name: oa-rdepot-app entrypoint: java -jar /opt/rdepot/rdepot.war volumes: - repositories:/opt/rdepot/repositories/ - snapshots:/opt/rdepot/generated/ - queue:/opt/rdepot/new/ - ./docker/app/authentication.yml:/opt/rdepot/authentication.yml - ./docker/app/application.yml:/opt/rdepot/application.yml networks: - oa-rdepot depends_on: - db environment: - DB_URL=jdbc:postgresql://oa-rdepot-db:5432/rdepot - DB_USERNAME=rdepot - DB_PASSWORD=mysecretpassword healthcheck: test: ["CMD-SHELL", "if [ \"$$(curl -I localhost:8080 2>/dev/null | grep HTTP/1.1 | cut -d\" \" -f2)\" != \"302\" ]; then exit 1; else exit 0; fi;"] interval: 10s timeout: 10s retries: 10 repo: image: openanalytics/rdepot-repo:1.4.2 restart: unless-stopped hostname: oa-rdepot-repo container_name: oa-rdepot-repo volumes: - repository:/opt/rdepot/ networks: - oa-rdepot networks: oa-rdepot: ipam: config: - subnet: 192.168.49.0/24 volumes: repository: repositories: snapshots: queue: logs:
The missing files (for volume mapping) can be found in our Git repository:
The final step is to launch the Docker containers using docker-compose:
docker-compose up -d
One can then go to http://localhost to log in.
There is an admin user with username
einstein and password
See authentication.yml for the included configuration which specifies the user credentials. One can override these parameters using environment variables.
To complete an end-to-end flow: R package to R Depot to Repository Server to R client, the following steps are needed:
- create a repository with (or edit)
- submit one or more packages to that repository via the R Depot web interface
- publish the repository using the green button in the repositories view (if needed)
- go to the published package page (repositories view, click repository name, click package name)
- use the install URL shown on the published package page to install the package in R
install.packages("somePackage", repos = c("http://localhost/repo/repositoryName", getOption()))
To (re)start with fresh database:
- remove the containers via
docker-compose down -v
- start up again using
docker-compose up -d
Kustomize is a tool for template-free configuration of applications running in Kubernetes. It offers a purely declarative approach to configuration customization.
Base recipes and a number of overlays are available for RDepot here.
The recipes are tagged according to the compatible RDepot release version and should be stable to use as a remote base:
apiVersion: kustomize.config.k8s.io/v1beta1 kind: Kustomization resources: - github.com/openanalytics/rdepot-kubernetes/base/app-stateful?ref=1.4.2 - github.com/openanalytics/rdepot-kubernetes/base/repo?ref=1.4.2
You can also clone the bases locally, copy the recipes or use a tool like kpt depending on the amount of independence you want to have w.r.t. the OpenAnalytics upstream.
Next to the base recipes you can find a number of overlays which range from simple extensions on top of the base recipes to complete demo deployments. The example below uses one of these overlays.
There are currently no plans to maintain RDepot helm charts from OpenAnalytics.
The following prerequisites are needed:
kustomizebinary is recommended as some features are used which are not available in the version included with
minikube is a distribution of Kubernetes that can easily run on a single machine with moderate resources.
To deploy the demo:
kubectl create namespace demo-rdepot kustomize build github.com/openanalytics/rdepot-kubernetes/overlays/demo?ref=1.4.2 | kubectl apply -f -
The demo includes:
- an instance of the RDepot repository server
- an instance of RDepot manager, preconfigured with a
demorepository on the repository server and protected with simple authentication
- a single-node postgres deployment
All volumes are provided through the dynamic provisioning in minikube
You can port-forward the manager app:
kubectl -n demo-rdepot port-forward svc/rdepot-app 8080:80
and visit the app in your browser at http://localhost:8080 (login
Similarly, you can port-forward the repository:
kubectl -n demo-rdepot port-forward svc/rdepot-repo 8081:80
and point your browser to http://localhost:8081/repo/demo to browse your uploaded packages.
You can tear down the demo with:
kubectl delete namespace demo-rdepot
Refer to the README for more info.
WAR & JAR
The latest versions of RDepot are available on our downloads page in WAR and JAR format.
This is currently not the recommended approach to deploy RDepot. This route is only relevant in the following cases:
- you wish to develop and/or extend RDepot
- you are not able to run docker on your platform of choice
Download both rdepot-app-1.4.2-application.war (sha256, md5) and rdepot-repo-1.4.2-application.jar (sha256, md5) and start them by executing
java -jar rdepot-app-1.4.2-application.war and
java -jar rdepot-repo-1.4.2-application.jar respectively.