nturaga / biockubeinstall

Build Bioconductor package binaries using Kubernetes on GKE or AKS

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 - [email protected]

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

BiocManager::install('Bioconductor/AnVIL')

## Should show the Google storage api as the top result
AnVIL::repositories()

AnVIL::install('Rhtslib')