Beyond
Regular
Galaxy
Management
Running Galaxy and Pulsar on Kubernetes the way it should be — native K8s jobs, RabbitMQ messaging, zero DinD, production-grade. Built in the Loire Valley, deployed on OVH PCI-DSS Cloud.
Galaxy jobs.
Kubernetes pods.
A custom queued_kubernetes manager for Pulsar that submits Galaxy jobs as native K8s batch/v1 Jobs via pykube — no Docker socket, no DinD, no privilege escalation.
Each Galaxy job becomes a real Kubernetes Job, scheduled by the cluster, monitored natively, with proper resource limits and a shared RWX NFS PVC for staging.
What's different
No more Docker socket. No more DinD. Real Kubernetes-native job execution.
Native K8s Jobs
Each Galaxy job maps to a real Kubernetes batch/v1 Job. Visible in kubectl, scheduled by the cluster, respecting node selectors and resource quotas.
No privileged containers
DinD required a privileged sidecar running dockerd inside a pod. Gone. The Pulsar pod has a standard ServiceAccount with scoped RBAC — nothing more.
RabbitMQ messaging
Galaxy publishes to AMQP, Pulsar consumes asynchronously. Job status flows back via MQ callbacks. No polling, no timeouts on long-running bioinformatics jobs.
Shared NFS staging
Pulsar and job pods mount the same RWX PVC. Inputs, outputs, scripts — all on shared NFS. No remote transfer overhead between galaxy and compute.
Helm-native deployment
Full Helm chart with configurable managers, RBAC, PVC, and Pulsar configuration via values.yaml. Reproducible, versionable, GitOps-ready.
Open source contribution
The queued_kubernetes manager is a genuine upstream contribution to galaxyproject/pulsar — autodiscovered, pattern-compliant, ready for PR.
PotamLigerien
Loire Valley · brgm.dev