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).
While the chart is still compatible with Helm 2, we highly recommend you start
using Helm 3 since we will not keep supporting Helm 2 going forward.
For Helm 2 installation, you will need to replace helm install my-galaxy-release
with helm install --name my-galaxy-release in all the commands below.
This Helm chart bootstraps a Galaxy deployment on a Kubernetes cluster. The chart allows application configuration changes, updates, upgrades, and rollbacks.
- Kubernetes 1.16+
- Helm 3+
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 can rely on the use of the CVMFS-CSI 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
- Galaxy-CVMFS-CSI (optional)
Launching from the source:
git clone https://github.com/galaxyproject/galaxy-helm.git
cd galaxy-helm/galaxy
helm dependency update
helm install my-galaxy-release .Launching from the repository of packaged charts:
helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/
helm repo update
helm install my-galaxy-release cloudve/galaxyhelm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/
helm repo update
helm install my-galaxy-release cloudve/galaxy --set cvmfs.enabled=true --set cvmfs.deploy=trueNOTE: It is not advisable to run multiple instances of the CVMFS-CSI simultaneously on the same cluster. If you wish to deploy multiple instances of Galaxy on the same cluster, please install the CVMFS-CSI chart separately as shown below. One exception to this is installing multiple releases of Galaxy in different namespaces AND running on different nodepools. In that case, it is possible to have each Galaxy release deploy its own CVMFS-CSI (and own NFS provisioner if desired). For that case, please refer to the GalaxyKubeMan Chart.
helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/
helm repo update
helm install cvmfs cloudve/galaxy-cvmfs-csi --namespace cvmfs --create-namespace
helm install my-galaxy-release-1 cloudve/galaxy --set cvmfs.enabled=true --set cvmfs.deploy=false --set ingress.path="/galaxy1/"
helm install my-galaxy-release-2 cloudve/galaxy --set cvmfs.enabled=true --set ingress.path="/galaxy2/"Note: cvmfs.deploy defaults to false. The explicit mention in the first release is
purely visual to highlight the difference.
- 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
my-galaxy(note the trailing dot):
helm install my-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 delete my-galaxyThe following table lists the configurable parameters of the Galaxy chart. The
current default values can be found in values.yaml file.
| Parameter | Description |
|---|---|
nameOverride |
Override the name of the chart used to prefix resource names. Defaults to {{.Chart.Name}} (i.e. galaxy) |
fullNameOverride |
Override the full name used to prefix resource names. Defaults to {{.Release.Name}}-{{.Values.nameOverride}} |
image.repository |
The repository and name of the Docker image for Galaxy, searches Docker Hub by default |
image.tag |
Galaxy Docker image tag (generally corresponds to the desired Galaxy version) |
image.pullPolicy |
Galaxy image pull policy for more info |
service.type |
Kubernetes Service type |
service.port |
Kubernetes service port |
service.nodePort |
If service.type is set to NodePort, then this can be used to set the port at which Galaxy will be available on all nodes' IP addresses |
webHandlers.replicaCount |
The number of replicas for the Galaxy web handlers |
webHandlers.annotations |
Additional annotations for the Galaxy web handlers at the Deployment level |
webHandlers.podAnnotations |
Additional annotations for the Galaxy web handlers at the Pod level |
webHandlers.podSpecExtra |
Additional specs for the Galaxy web handlers at the pod level |
webHandlers.readinessProbe.enabled |
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 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" galaxyYou can also set the galaxy configuration file in its entirety with:
helm install --set-file "configs.galaxy\.yml"=/path/to/local/galaxy.yml galaxyTo unset an existing file and revert to the container's default version:
helm install --set-file "configs.job_conf\.xml"=null galaxyAlternatively, a YAML file that specifies the values of the parameters can be provided when installing the chart. For example,
helm install 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 a values file that supports CVMFS support out-of-the-box. 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 need to enable CVMFS deployment. Depending on the setup of the cluster you have available, you may also need to supply values for the cluster storage classes or PVCs.
If you wish to install a single Galaxy CVMFS-CSI release to be used by multiple Galaxy releases, you can do so by installing the CVMFS separately as shown below:
helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/
helm repo update
kubectl create namespace cvmfs
helm install cvmfs --namespace cvmfs cloudve/galaxy-cvmfs-csi
# Download values-cvmfs.yaml from this repo and update persistence as needed
helm install galaxy cloudve/galaxy -f values.yaml --set cvmfs.enabled=true --set cvmfs.deploy=falseIf you wish to get a quick deployment of a single Galaxy instance with its own CVMFS-CSI, you can do so by enabling the CVMFS deployment as part of this chart:
helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/
helm repo update
kubectl create namespace cvmfs
helm install cvmfs --namespace cvmfs cloudve/galaxy-cvmfs-csi
# Download values-cvmfs.yaml from this repo and update persistence as needed
helm install galaxy cloudve/galaxy -f values.yaml --set cvmfs.enabled=true --set cvmfs.deploy=trueIf you use the latter method, it is highly recommended that you deploy a single Galaxy release per nodepool, as multiple CVMFS-CSI provisioners running on the same node can cause conflicts.
Once started, Galaxy will be available under /galaxy/ (note the trailing /).
This path can be changed by setting the value: `--set ingress.path="/mynewgalaxypath/"
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.