vip-web

Variant Interpretation Pipeline web interface, available at https://vip.molgeniscloud.org.

Developers

Repository consists of three projects:

• vip-web-backend
• vip-web-cluster
• vip-web-frontend

Application flow:

• Users create jobs using the vip-web-frontend
• Jobs are stored in the vip-web-backend database
• Compute cluster(s) can use the scripts in vip-web-cluster to poll vip-web-backend for the next available job
• The cluster processes the job using VIP
• The cluster sends back the results to VIP

The backend is not aware of the existence of any clusters, all communication is initiated by the compute cluster(s).

Development

Backend

Requirements

• Java 21

Running

java -Dspring.profiles.active=dev org.molgenis.vipweb.VipWebApplication

Frontend

pnpm run dev

Build

mvn clean install

Deployment

Backend & Frontend

VIPWEB_ADMIN_USERNAME=<username> \
VIPWEB_ADMIN_PASSWORD=<password> \
VIPWEB_DATASOURCE_URL=jdbc:h2:file:<path>/h2 \
VIPWEB_DATASOURCE_USERNAME=<username> \
VIPWEB_DATASOURCE_PASSWORD=<password> \
VIPWEB_FS_PATH=<path> \
VIPWEB_INITIALIZER_ENABLED=true \
VIPWEB_INITIALIZER_JOBS=<path_to_json> \
VIPWEB_INITIALIZER_TREES=<path_to_json> \
VIPWEB_REMEMBERME_KEY=<key> \
VIPWEB_SQL_INIT_MODE=always \
VIPWEB_VIPBOT_USERNAME=<username> \
VIPWEB_VIPBOT_PASSWORD=<password> \
java -jar -Dspring.profiles.active=production vip-web-backend-<version>.jar

Cluster

Follow https://github.com/molgenis/vip to install VIP on a cluster.

git clone https://github.com/molgenis/vip-web
cd vip-web/vip-web-cluster
VIPWEB_VIPBOT_USERNAME=<username> VIPWEB_VIPBOT_PASSWORD=<password> VIP_DIR=<path> bash run.sh

Example cron job that checks for work every minute:

* * * * * VIPWEB_VIPBOT_USERNAME=<username> VIPWEB_VIPBOT_PASSWORD=<password> VIP_DIR=<path> /usr/bin/flock -n <path>/vip-web.lockfile /bin/bash <path>/vip-web/vip-web-cluster/run.sh >> <path>/cron.log 2>&1