Galaxy Helm Chart (v3)

Galaxy is a data analysis platform focusing on accessibility, reproducibility, and transparency of primarily bioinformatics data. This repo contains Helm charts for easily deploying Galaxy on top of Kubernetes.

You may follow this documentation on how to use this Helm chart to deploy Galaxy on various managed kubernetes services (e.g., Amazon EKS and Google GKE).

TL;DR

git clone https://github.com/galaxyproject/galaxy-helm.git
cd galaxy-helm/galaxy
helm dependency update
helm install .

Introduction

This Helm chart bootstraps a Galaxy deployment on a Kubernetes cluster. The chart allows application configuration changes, updates, upgrades, and rollbacks.

Prerequisites

• Kubernetes 1.13+
• Helm 2.10+

You will need a Kubernetes and Helm installation; the easiest option for testing and development purposes is to install Docker Desktop, which comes with integrated Kubernetes. You will also need to install Helm.

Dependency Charts

This chart relies on the features of other charts for common functionality. Most notably, this includes the Postgres chart for the database. In addition, the chart relies on the use of the CVMFS chart for linking the reference data to Galaxy and jobs. While, technically, CVMFS is an optional dependency, production settings will likely want it enabled.

• Postgres
• CVMFS (optional)

Installing the Chart

1. Clone this repository and install the required dependency charts.

git clone https://github.com/galaxyproject/galaxy-helm.git
cd galaxy-helm/galaxy
helm dependency update

2. To install the chart with the release name galaxy (note the trailing dot):

helm install --name galaxy .

In about a minute, Galaxy will be available at the root URL of your kubernetes cluster.

Uninstalling the Chart

To uninstall/delete the galaxy deployment, run:

helm del --purge galaxy

Configuration

The following table lists the configurable parameters of the Galaxy chart. The current default values can be found in values.yaml file.

Parameter	Description
image.repository	The repository and name of the Docker image for Galaxy pointing to Docker Hub.
image.tag	Galaxy image tag / version
image.pullPolicy	Galaxy image pull policy
service.type	Kubernetes Service type, ClusterIP by default.
service.port	Galaxy service port
service.nodePort	If service.type set to NodePort, then this can be used to set the port at which Galaxy will be available on all nodes' IP addresses. 30700 by default.
webHandlers.replicaCount	The number of replicas for the Galaxy web handlers
jobHandlers.replicaCount	The number of replicas for the Galaxy job handlers
rbac.enabled	Enable Galaxy job RBAC
persistence.enabled	Enable persistence using PVC
persistence.name	Name of the PVC
persistence.storageClass	PVC Storage Class for Galaxy volume (use either this or existingClaim)
persistence.existingClaim	An existing PVC to be used for the Galaxy volume (use either this or storageClass)
persistence.accessMode	PVC access mode for the Galaxy volume
persistence.size	PVC storage request for the Galaxy volume, in GB
persistence.mountPath	Path where to mount the Galaxy volume
extraEnv	Any extra environment variables you would like to pass on to the pod
ingress.enabled	Enable Kubernetes ingress
ingress.path	Path where Galaxy application will be hosted
ingress.hosts	Cluster hosts where Galaxy will be available
useSecretConfigs	Enable Kubernetes Secrets for all config maps
configs.*	Galaxy configuration files and values for each of the files. The provided value represent the entire content of the given configuration file
jobs.rules	Galaxy dynamic job rules
postgresql.galaxyDatabaseUser	Postgresql user for Galaxy database
postgresql.galaxyDatabasePassword	Password for Galaxy's postgresql user. This is not set by default and a random password is generated by Helm.
postgresql.galaxyExistingSecret	Overrides galaxyDatabasePassword. Use password from an exiting secret for Galaxy's postgresql user
postgresql.galaxyExistingSecretKeyRef	Key for data portion containing the password from galaxyExistingSecret. Defaults to galaxy-db-password

Specify each parameter using the --set key=value[,key=value] argument to helm install. For example,

helm install --name galaxy --set persistence.size=50 .

The above command sets the Galaxy persistent volume to 50GB.

Setting Galaxy configuration file values requires the key name to be escaped:

helm install --set-file "configs.galaxy\.yml.brand"="Hello World"

You can also set the galaxy configuration file in its entirety with:

helm install --set-file "configs.galaxy\.yml"=/path/to/local/galaxy.yml

To unset an existing file and revert to the container's default version:

helm install --set-file "configs.job_conf\.xml"=null

Alternatively, a YAML file that specifies the values of the parameters can be provided when installing the chart. For example,

helm install --name galaxy -f values-cvmfs.yaml .

To unset a config file, use the yaml null type:

configs:
  job_conf.xml: ~

Data Persistence

The Galaxy Docker image stores all user data under /galaxy/server/database path of the container. Persistent Volume Claims (PVCs) are used to keep the data across deployments. It is possible to specify en existing PVC via persistence.existingClaim. Alternatively, a value for persistence.storageClass can be supplied to designate a desired storage class for dynamic provisioning of the necessary PVCs. If neither value is supplied, the default storage class for the k8s cluster will be used.

We recommend a storage class that supports ReadWriteMany, such as the nfs-provisioner as the data must be available to all nodes in the cluster.

In addition, we recommend that you also set postgresql.persistence.storageClass to a high-speed, durable storage type that is ReadWriteOnce, such as an EBS volume.

Note about persistent deployments and restarts

If you wish to make your deployment persistent or restartable (bring deployment down, keep the state in disk, then bring it up again later in time), you should create PVCs for Galaxy and Postgres and use the existingClaims variables to point to them as explained in the previous section. In addition, you MUST set the postgresql.galaxyDatabasePassword and postgresql.postgresqlPassword variables, as on a restart from the existing PVCs the Helm random password used for those slot won't be maintained, breaking database access.

To start a new deployment from PVCs that belonged to a previous deployment on a different cluster, you might need to disable the database init part by setting postgresql.initdbScriptsSecrets: null.

What if we didn't set db passwords in the first place

You can allow trusted local connections and then use that to enter the postgresql server and change passwords. To allow trusted connections, set the pg_hba.conf file through:

postgresql:
  pgHbaConfiguration: |
    host     all             all             0.0.0.0/0               md5
    host     all             all             ::1/128                 md5
    local    all             all                                     trust

Production Settings

This repo contains an additional values file with the production settings, called values-cvmfs.yaml. This mode of deployment configures Galaxy with the data from CMVFS and replicates the functional capabilities of the Galaxy Main server. Note that this deployment mode does not work on a Mac laptop because of an unresolved issue in the CVMFS-CSI docker container.

To install this version of the chart, we first need to install the Galaxy CVMFS-CSI chart, followed by the Galaxy chart. Depending on the setup of the cluster you have available, you may also need to supply values for the cluster storage classes or PVCs.

helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/
helm repo update
kubectl create namespace cvmfs
helm install --name cvmfs --namespace cvmfs cloudve/galaxy-cvmfs-csi
# Download values-cvmfs.yaml from this repo and update persistence as needed
helm install --name galaxy -f values-cvmfs.yaml cloudve/galaxy

Note that this setup takes several minutes to start due to Galaxy loading all the tool definitions. Once started, Galaxy will be available under /galaxy/ (note the trailing / as it is required).

Horizontal Scaling

The Galaxy application can be horizontally scaled for the web and job handlers by setting the desired values of the webHandlers.replicaCount and jobHandlers.replicaCount configuration options.

Funding

• Version 3: Galaxy Project, Genomics Virtual Laboratory (GVL)

• Version 2: Genomics Virtual Laboratory (GVL), Galaxy Project, and European Commission (EC) H2020 Project PhenoMeNal, grant agreement number 654241.

• Version 1: European Commission (EC) H2020 Project PhenoMeNal, grant agreement number 654241.