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).
git clone https://github.com/galaxyproject/galaxy-helm.git
cd galaxy-helm/galaxy
helm dependency update
helm install .This Helm chart bootstraps a Galaxy deployment on a Kubernetes cluster. The chart allows application configuration changes, updates, upgrades, and rollbacks.
- 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.
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)
- 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- 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.
To uninstall/delete the galaxy deployment, run:
helm del --purge galaxyThe 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.ymlTo unset an existing file and revert to the container's default version:
helm install --set-file "configs.job_conf\.xml"=nullAlternatively, 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: ~
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.
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.
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
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/galaxyNote 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).
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.
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Version 3: Galaxy Project, Genomics Virtual Laboratory (GVL)
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Version 2: Genomics Virtual Laboratory (GVL), Galaxy Project, and European Commission (EC) H2020 Project PhenoMeNal, grant agreement number 654241.
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Version 1: European Commission (EC) H2020 Project PhenoMeNal, grant agreement number 654241.