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BiocKubeInstall

Internal Bioconductor package used to create binaries for docker images produced by Bioconductor. The package installation and binary creation is parallelized on a Kubernetes cluster launched (at the moment) on a Kubernetes cluster using GKE.

The package works in sync with the Bioconductor/k8sredis kubernetes application.

Author

Nitesh Turaga - nturaga.bioc@gmail.com

Martin Morgan

Links

k8sredis: www.github.com/Bioconductor/k8sredis

Vignette: BiocKubeInstall_Tutorial

Components

  1. inst/helm-chart : helm chart for k8s app

  2. inst/docker : docker images used inside the k8s application

  3. BiocKubeInstall R/ : Code which runs on the manager and worker replica sets.

  4. Github Actions: Start cluster and deploy to cluster, delete cluster, and test binary package installs 3 times a week.

Usage for AnVIL platform and all bioconductor_docker inherited images

Install binary packages using BiocManager::install

BiocManager::install('Rhtslib')