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Instalation TOBIAS Kubernetes S3 Version
To run the Pipeline you need a S3 Account and a Kuberntes Account. If you have an Kuberntesaccount go to the Rancher Website of your Cluster and get the accssesconfiguration key. Store this key under '~/.kube/config'.
The setup of the cluster has been automated with a python skript it creats the required persisten volume claim on the cluster and stores the S3 credentials in secrets on the Cluster.
The Persisten Volume Claim is a managed-nfs-storage so a nfs storage must be available on the cluster. The pvc get's name 'nextflowpvc' with a szie of 250Gib if their is allready 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 an other name for the pvc specity this with --pvc_name by runnig 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.
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 informations, such as passwords and SSH keys. The default name of the secret createt by the setup skript id s3mpi. If you want to change it set --secretname when runing the setup skript and change the name of the secret in the config file of the pipeline.