Instalation TOBIAS Kubernetes S3 Version

To run the Pipeline you need a S3 Account and a Kubernetesaccount. If you have, a Kuberntesaccount go to the Rancher Website of your Cluster and get the access configuration key. Store this key under '~/.kube/config'

Setup the Cluster

The setup of the cluster has been automated with a python script it creates the required persistent volume claim on the cluster and stores the S3 credentials in secrets on the Cluster.

Persisten Volume Claim

The Persistent Volume Claim is a managed-nfs-storage so an nfs storage must be available on the cluster. The pvc gets name 'nextflowpvc' with a size of 250Gib if there is already a pvc called 'nextflowpvc' the script will ask you if it should replace the pvc (If you replace the pvc all your files in the current pvc get lost!). If you want to use another name for the pvc specify this with --pvc_name by running the setupskript. Then you must change also the name of the PVC in the config file of the pipeline. For more information look at link.

S3-Secret

The S3 credentials must be available on the cluster so that the Jobs are able to download and upload the files to the S3. The credentials are stored on secretes on the cluster. Secrets are objects on the cluster, which contain sensitive information’s, such as passwords and SSH keys. The default name of the secret created by the setup script id s3mpi. If you want to change it set --secretname when running the setup script and change the name of the secret in the config file of the pipeline. For more information look at link