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Implementation TOBIAS Kubernetes S3 Version

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goymann edited this page Sep 19, 2019 · 19 revisions

Running Jobs on Kubernetes

To run a job you have to send a yaml with the congurations to the cluster. To get the les for calculating to the cluster and the results back to your local machine you need the S3-Storage. First you upload your Data to the S3 then the job on the cluster starts and downloads the les from the S3. When calculation has nished the job uploads the results to the S3 and then your VM can download the results from the S3 to your machine.

Vortrag_TOBIAS_nextflow_Kubernetes_3

How the pipeline works

The most time-consuming part of calculating jobs on the cluster is transfer- ring the data through the S3-Storage to the Cluster. For these reasons the bigwig les are storage on the cluster in a NFS Storage so that every pod can get the les from their. The piloting on Kubernetes is split in to 3 processes.

1. In the rst process the bigwig les from the ATaCcoreect are sending
   to the NFS volume on the cluster.

Step1

2. When the biwigs are present on the NFS the pipeline starts the plotting on the Cluster. All plots for one         
   motive run in one Pod. When the plotting has nished the Plots get upload to the S3-Storage.

Step2

3. In the last step when a Pod on the Cluster has nished the les get back download form the S3 to your VM.

Step3

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