Galaxy is a data analysis platform focusing on accessibility, reproducibility, and transparency of primarily bioinformatics data. This repo contains a Helm chart for easily deploying Galaxy on top of Kubernetes. The chart allows application configuration changes, updates, upgrades, and rollbacks.
- Kubernetes 1.27+
- Helm 3.5+
You will need kubectl (instructions)
and Helm (instructions) installed.
For testing and development purposes, an easy option to get Kubernetes running
is to install Rancher Desktop. Once you have it
installed, you will also need to setup an ingress controller. Rancher uses
Traefik as the default one, so disable it first by unchecking Enable Traefik
from the Kubernetes Settings page. Then deploy the NGINX ingress controller:
helm upgrade --install ingress-nginx ingress-nginx \
--repo https://kubernetes.github.io/ingress-nginx \
--namespace ingress-nginx --create-namespace
This chart relies on the features of other charts for common functionality:
- postgres-operator for the database;
- galaxy-cvmfs-csi for linking the reference data to Galaxy and jobs based on CVMFS (default).
- csi-s3 for linking reference data to Galaxy and jobs based on S3FS (optional/alternative to CVMFS).
- rabbitmq-cluster-operator for deploying the message queue.
In a production setting, especially if the intention is to run multiple Galaxies
in a single cluster, we recommend installing the dependency charts separately
once per cluster, and installing Galaxy with --set postgresql.deploy=false --set s3csi.deploy=false --set cvmfs.deploy=false --set rabbitmq.deploy=false.
- The chart is automatically packaged, versioned and uploaded to a helm repository on each accepted PR. Therefore, the latest version of the chart can be downloaded from this repository.
helm repo add cloudve https://raw.githubusercontent.com/CloudVE/helm-charts/master/
helm repo update- Install the chart with the release name
my-galaxy. It is not advisable to install Galaxy in thedefaultnamespace.
helm install my-galaxy-release cloudve/galaxy- Clone this repository and add 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. See Data persistence section below about the use of persistence flag that is suitable for your Kubernetes environment.
helm install --create-namespace -n galaxy my-galaxy . --set persistence.accessMode="ReadWriteOnce"In several minute, Galaxy will be available at /galaxy/ URL of your Kubernetes
cluster. If you are running the development Kubernetes, Galaxy will be available
at http://localhost/galaxy/ (note the trailing slash).
To uninstall/delete the my-galaxy deployment, run:
helm delete my-galaxyif you see that some RabbitMQ and Postgres elements remain after some 10 minutes or more, you should be able to issue:
kubectl delete RabbitmqCluster/my-galaxy-rabbitmq-server
kubectl delete statefulset/galaxy-my-galaxy-postgres
it might be needed to remove the finalizer from the RabbitmqCluster if the above doesn't seem to get rid of RabbitmqCluster, through a
kubectl edit RabbitmqCluster/my-galaxy-rabbitmq-server
remove the finalizer in:
apiVersion: rabbitmq.com/v1beta1
kind: RabbitmqCluster
metadata:
annotations:
meta.helm.sh/release-name: my-galaxy
meta.helm.sh/release-namespace: default
creationTimestamp: "2022-12-19T16:54:33Z"
deletionGracePeriodSeconds: 0
deletionTimestamp: "2022-12-19T17:41:40Z"
finalizers:
- deletion.finalizers.rabbitmqclusters.rabbitmq.com
and remove the postgres secret:
kubectl delete secrets/standby.galaxy-my-galaxy-postgres.credentials.postgresql.acid.zalan.do
Consider as well that if you set persistence to be enabled, Postgres and Galaxy will leave their PVCs behind, which you might want to delete or not depending on your use case.
The following table lists the configurable parameters of the Galaxy chart. The
current default values can be found in values.yaml file.
| Parameters | Description |
|---|---|
nameOverride |
Override the name of the chart used to prefix resource names. Defaults to {{.Chart.Name}} (e.g., galaxy) |
fullnameOverride |
Override the full name used to prefix resource names. Defaults to {{.Release.Name}}-{{.Values.nameOverride}} |
image.pullPolicy |
Galaxy image pull policy for more info |
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) |
imagePullSecrets |
Secrets used to access a Galaxy image from a private repository |
persistence.enabled |
Enable persistence using PVC |
persistence.size |
PVC storage request for the Galaxy volume, in GB |
persistence.accessMode |
PVC access mode for the Galaxy volume |
persistence.annotations.{} |
Dictionary of annotations to add to the persistent volume claim's metadata |
persistence.existingClaim |
Use existing Persistent Volume Claim instead of creating one |
persistence.storageClass |
Storage class to use for provisioning the Persistent Volume Claim |
persistence.name |
Name of the PVC |
persistence.mountPath |
Path where to mount the Galaxy volume |
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.priorityClass.enabled |
Assign a priorityClass to the dispatched jobs. |
jobs.rules |
Galaxy dynamic job rules. See values.yaml |
jobs.priorityClass.existingClass |
Use an existing priorityClass to assign if jobs.priorityClass.enabled=true |
refdata.enabled |
Whether or not to mount cloud-hosted Galaxy reference data and tools. |
refdata.type |
s3fs or cvmfs, determines the CSI to use for mounting reference data. s3fs is the default and recommended for the time being. |
s3csi.deploy |
Deploy the CSI-S3 Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource. |
cvmfs.deploy |
Deploy the Galaxy-CVMFS-CSI Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource |
cvmfs.enabled |
Enable use of CVMFS in configs, and deployment of CVMFS Persistent Volume Claims for Galaxy |
cvmfs.pvc.{} |
Persistent Volume Claim to deploy for CVMFS repositories. See values.yaml for examples. |
setupJob.ttlSecondsAfterFinished |
Sets ttlSecondsAfterFinished for the initialization jobs. See the Kubernetes documentation for more details. |
setupJob.downloadToolConfs.enabled |
Download configuration files and the tools directory from an archive via a job at startup |
setupJob.downloadToolConfs.archives.startup |
A URL to a tar.gz publicly accessible archive containing AT LEAST conf files and XML tool wrappers. Meant to be enough for Galaxy handlers to startup. |
setupJob.downloadToolConfs.archives.running |
A URL to a tar.gz publicly accessible archive containing AT LEAST confs, tool wrappers, and tool scripts but excluding test data. Meant to be enough for Galaxy handlers to run jobs. |
setupJob.downloadToolConfs.archives.full |
A URL to a tar.gz publicly accessible archive containing the full tools directory, including each tool's test data. Meant to be enough to run automated tool-tests, fully mimicking CVMFS repositories |
setupJob.downloadToolConfs.volume.mountPath |
Path at which to mount the unarchived confs in the each handler (should match path set in the tool confs) |
setupJob.downloadToolConfs.volume.subPath |
Name of subdirectory on Galaxy's shared filesystem to use for the unarchived configs |
setupJob.createDatabase |
Deploy a job to create a Galaxy database from scratch (does not affect subsequent upgrades, only first startup) |
ingress.path |
Path where Galaxy application will be hosted |
ingress.annotations.{} |
Dictionary of annotations to add to the ingress's metadata at the deployment level |
ingress.hosts |
Hosts for the Galaxy ingress |
ingress.canary.enabled |
This will create an additional ingress for detecting activity on Galaxy. Useful for autoscaling on activity. |
ingress.enabled |
Enable Kubernetes ingress |
ingress.tls |
Ingress configuration with HTTPS support |
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 |
service.port |
Kubernetes service port |
service.type |
Kubernetes Service type |
serviceAccount.annotations.{} |
Dictionary of annotations to add to the service account's metadata |
serviceAccount.create |
The serviceAccount will be created if it does not exist. |
serviceAccount.name |
The serviceAccount account to use. |
rbac.enabled |
Enable Galaxy job RBAC. This will grant the service account the necessary permissions/roles to view jobs and pods in this namespace. Defaults to true. |
webHandlers.{} |
Configuration for the web handlers (See table below for all options) |
jobHandlers.{} |
Configuration for the job handlers (See table below for all options) |
workflowHandlers.{} |
Configuration for the workflow handlers (See table below for all options) |
resources.limits.memory |
The maximum memory that can be allocated. |
resources.requests.memory |
The requested amount of memory. |
resources.limits.cpu |
The maximum CPU that can be alloacted. |
resources.limits.ephemeral-storage |
The maximum ephemeral storage that can be allocated. |
resources.requests.cpu |
The requested amount of CPU (as time or number of cores) |
resources.requests.ephemeral-storage |
The requested amount of ephemeral storage |
securityContext.fsGroup |
The group for any files created. |
tolerations |
Define the taints that are tolerated. |
extraFileMappings.{} |
Add extra files mapped as configMaps or Secrets at arbitrary paths. See values.yaml for examples. |
extraInitCommands |
Extra commands that will be run during initialization. |
extraInitContainers.[] |
A list of extra init containers for the handler pods |
extraVolumeMounts.[] |
List of volumeMounts to add to all handlers |
extraVolumes.[] |
List of volumes to add to all handlers |
postgresql.enabled |
Enable the postgresql condition in the requirements.yml. |
influxdb.username |
Influxdb user name. |
influxdb.url |
The connection URL to in the influxdb |
influxdb.enabled |
Enable the influxdb used by the metrics scraper. |
influxdb.password |
Password for the influxdb user. |
metrics.podAnnotations.{} |
Dictionary of annotations to add to the metrics deployment's metadata at the pod level |
metrics.image.repository |
The location of the galay-metrics-scraping image to use. |
metrics.image.pullPolicy |
Define the pull policy, that is, when Kubernetes will pull the image. |
metrics.podSpecExtra.{} |
Dictionary to add to the metrics deployment's pod template under spec |
metrics.image.tag |
The image version to use. |
metrics.annotations.{} |
Dictionary of annotations to add to the metrics deployment's metadata at the deployment level |
metrics.enabled |
Enable metrics gathering. The influxdb setting must be specified when using this setting. |
nginx.conf.client_max_body_size |
Requests larger than this size will result in a 413 Payload Too Large. |
nginx.image.tag |
The Nginx version to pull. |
nginx.image.repository |
Where to obtain the Nginx container. |
nginx.image.pullPolicy |
When Kubernetes will pull the Nginx image from the repository. |
nginx.galaxyStaticDir |
Location at which to copy Galaxy static content in the NGINX pod init container, for direct serving. Defaults to /galaxy/server/static |
Galaxy defines three handler types: jobHandlers, webHandlers, and
workflowHandlers. All three handler types share common configuration options.
| Parameter | Description |
|---|---|
replicaCount |
The number of handlers to be spawned. |
startupDelay |
Delay in seconds for handler startup. Used to offset handlers and avoid race conditions at first startup |
annotations |
Dictionary of annotations to add to this handler's metadata at the deployment level |
podAnnotations |
Dictionary of annotations to add to this handler's metadata at the pod level |
podSpecExtra |
Dictionary to add to this handler's pod template under spec |
startupProbe |
Probe used to determine if a pod has started. Other probes wait for the startup probe. See table below for all probe options |
livenessProbe |
Probe used to determine if a pod should be restarted. See table below for all probe options |
readinessProbe |
Probe used to determine if the pod is ready to accept workloads. See table below for all probe options |
Kubernetes uses probes to determine the state of a pod. Pods are not considered
to have started up, and hence other probes are not run, until the startup probes
have succeeded. Pods that fail the livenessProbe will be restarted and work
will not be dispatched to the pod until the readinessProbe returns
successfully. A pod is ready when all of its containers are ready.
Liveness and readiness probes share the same configuration options.
| Parameter | Description |
|---|---|
enabled |
Enable/Disable the probe |
initialDelaySeconds |
How long to wait before starting the probe. |
periodSeconds |
How frequently Kubernetes with check the probe. |
failureThreshold |
The number of failures Kubernetes will retry the readiness probe before giving up. |
timeoutSeconds |
How long Kubernetes will wait for a probe to timeout. |
jobHandlers:
replicaCount: 2
livenessProbe:
enabled: false
readinessProbe:
enabled: true
initialDelaySeconds: 300
periodSecods: 30
timeoutSeconds: 5
failureThreshhold: 3
The extraFileMappings field can be used to inject files to arbitrary paths in the nginx deployment, as well as any of the job, web, or workflow handlers, and the init jobs.
The contents of the file can be specified directly in the values.yml file with the content attribute.
The tpl flag will determine whether these contents are run through the helm templating engine.
Note: when running with tpl: true, brackets ({{ }}) not meant for Helm should be escaped. One way of escaping is: {{ '{{ mynon-helm-content}}' }}
extraFileMappings:
/galaxy/server/static/welcome.html:
applyToWeb: true
applyToJob: false
applyToWorkflow: false
applyToNginx: true
applyToSetupJob: false
tpl: false
content: |
<!DOCTYPE html>
<html>...</html>NOTE for security reasons Helm will not load files from outside the chart so the path must be a relative path to location inside the chart directory. This will change when helm#3276 is resolved. In the interim files can be loaded from external locations by:
- Creating a symbolic link in the chart directory to the external file, or
- using
--set-fileto specify the contents of the file. E.g:helm upgrade --install galaxy cloudve/galaxy -n galaxy --set-file extraFileMappings."/galaxy/server/static/welcome\.html".content=/home/user/data/welcome.html --set extraFileMappings."/galaxy/server/static/welcome\.html".applyToWeb=true
Alternatively, if too many .applyTo need to be set, the apply flags can be inserted instead to the extraFileMappings (in addition to the --set-file in the cli) for that file in your values.yaml, with no content: part (as that is done through the --set-file):
extraFileMappings:
/galaxy/server/static/welcome.html:
applyToJob: false
applyToWeb: true
applyToSetupJob: false
applyToWorkflow: false
applyToNginx: false
tpl: false
Specify each parameter using the --set key=value[,key=value] argument to
helm install or helm upgrade. For example,
helm install my-galaxy . --set persistence.size=50GiThe above command sets the Galaxy persistent volume to 50GB.
Setting Galaxy configuration file values requires the key name to be escaped. In this example, we are upgrading an existing deployment.
helm upgrade my-galaxy . --set "configs.galaxy\.yml.brand"="Hello World"You can also set the galaxy configuration file in its entirety with:
helm install my-galaxy . --set-file "configs.galaxy\.yml"=/path/to/local/galaxy.ymlTo unset an existing file and revert to the container's default version:
helm upgrade my-galaxy . --set "configs.job_conf\.xml"=nullAlternatively, any number of YAML files that specifies the values of the parameters can be provided when installing the chart. For example,
helm install my-galaxy . -f values.yaml -f new-values.yamlTo unset a config file in a values file, use the YAML null type:
configs:
job_conf.xml: ~
By default, the Galaxy handlers store all user data under
/galaxy/server/database/ path in each container. This path can be changed via
persistence.mountPath variable. Persistent Volume Claims (PVCs) are used to
persist 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.
For multi-node scenarios, 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 single-node scenarios, you must use --set persistence.accessMode="ReadWriteOnce".
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 persistence.existingClaim
variable to point to them as explained in the previous section. In addition, you
must set the postgresql.galaxyDatabasePassword variable; otherwise, it will be
autogenerated and will mismatch when restoring.
In general, Interactive Tools should work out of the box as long as you have a
wildcard DNS mapping to *.its.<host_name>. To make Interactive Tools work on
localhost, you can use dnsmasq or similar to handle wildcard DNS mappings for
*.localhost.
For linux: Follow the instructions here to configure dnsmasq on Linux: https://superuser.com/a/1718296
For mac:
$ brew install dnsmasq
$ cp /usr/local/opt/dnsmasq/dnsmasq.conf.example /usr/local/etc/dnsmasq.conf
$ edit /usr/local/etc/dnsmasq.conf and set
address=/localhost/127.0.0.1
$ sudo brew services start dnsmasq
$ sudo mkdir /etc/resolver
$ sudo touch /etc/resolver/localhost
$ edit /etc/resolver/localhost and set
nameserver 127.0.0.1
$ sudo brew services restart dnsmasqThis should make all *.localhost and *.its.localhost map to 127.0.0.1, and ITs should work with a regular helm install on localhost.
The Galaxy application can be horizontally scaled for the web, job, or workflow handlers
by setting the desired values of the webHandlers.replicaCount,
jobHandlers.replicaCount, and workflowHandlers.replicaCount configuration options.
Two Cron jobs are defined by default. One to clean up Galaxy's database and one to clean up the tmp directory. By default, these
jobs run at 02:05 (the database maintenance script) and 02:15 (tmp directyory cleanup). Users can
change the times the cron jobs are run by changing the schedule field in the values.yaml file:
cronJobs:
maintenance:
schedule: "30 6 * * *" # Execute the cron job at 6:30 UTCor by specifying the schedule on the command line when instaling Galaxy:
# Schedule the maintenance job to run at 06:30 on the first day of each month
helm install galaxy -n galaxy galaxy/galaxy --set cronJobs.maintenance.schedule="30 6 1 * *"To disable a cron job after Galaxy has been deployed simply set the enabled flag for that job to false:
helm upgrade galaxy -n galaxy galaxy/galaxy --reuse-values --set cronJobs.maintenance.enabled=falseCron jobs can be invoked manually with tools such as OpenLens
or from the command line with kubectl
kubectl create job --namespace <namespace> <job name> --from cronjob/galaxy-cron-maintenance This will run the cron job regardless of the schedule that has been set.
Note: the name of the cron job will be {{ .Release.Name }}-cron-<job name> where the <job name>
is the name (key) used in the values.yaml file.
The following fields can be specified when defining cron jobs.
| Name | Definition | Required |
|---|---|---|
| enabled | true or false. If false the cron job will not be run. Default is true |
Yes |
| schedule | When the job will be run. Use tools such as crontab.guru for assistance determining the proper schedule string | Yes |
| defaultEnv | true or false. See the galaxy.podEnvVars macro in _helpers.tpl for the list of variables that will be defined. Default is false |
No |
| extraEnv | Define extra environment variables that will be available to the job | No |
| securityContext | Specifies a securityContext for the job. Typically used to set runAsUser |
No |
| image | Specify the Docker container used to run the job | No |
| command | The command to run | Yes |
| args | Any command line arguments that should be passed to the command |
No |
| extraFileMappings | Allow arbitrary files to be mounted from config maps | No |
If specifying the Docker image both the resposity and tag MUST be specified.
image:
repository: quay.io/my-organization/my-image
tag: "1.0" The extraFileMappings block is similar to the global extraFileMappings except the file will only be mounted for that cron job.
The following fields can be specified for each file.
| Name | Definition | Required |
|---|---|---|
| mode | The file mode (permissions) assigned to the file | No |
| tpl | If set to true the file contents will be run through Helm's templating engine. Defaults to false |
No |
| content | The contents of the file | Yes |
See the example cron job included in the values.yaml file for a full example.