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Open Source Science

https://github.com/bioconductor/biockubeinstall

Build Bioconductor package binaries using Kubernetes on GKE or AKS

https://github.com/bioconductor/biockubeinstall

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.2%) to scientific vocabulary

Keywords

kubernetes
Last synced: 9 months ago · JSON representation

Repository

Build Bioconductor package binaries using Kubernetes on GKE or AKS

Basic Info
  • Host: GitHub
  • Owner: Bioconductor
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 738 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 3
  • Open Issues: 2
  • Releases: 0
Topics
kubernetes
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

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')

Owner

  • Name: Bioconductor
  • Login: Bioconductor
  • Kind: organization

Software for the analysis and comprehension of high-throughput genomic data

GitHub Events

Total
  • Member event: 1
  • Push event: 5
  • Create event: 2
Last Year
  • Member event: 1
  • Push event: 5
  • Create event: 2

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 43
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 days
  • Total issue authors: 0
  • Total pull request authors: 5
  • Average comments per issue: 0
  • Average comments per pull request: 0.21
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • almahmoud (27)
  • nturaga (10)
  • Jiefei-Wang (3)
  • mtmorgan (2)
  • LiNk-NY (1)
Top Labels
Issue Labels
Pull Request Labels
bug (1)

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • AnVIL * imports
  • BiocManager * imports
  • BiocParallel * imports
  • RedisParam * imports
  • futile.logger * imports
  • methods * imports
  • redux * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/docker_image_build.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
.github/workflows/gcp_slack_check.yaml actions
  • google-github-actions/auth v1 composite
  • google-github-actions/setup-gcloud v1 composite
  • slackapi/slack-github-action v1.19.0 composite
.github/workflows/gke_run.yml actions
  • actions/checkout v2 composite
  • google-github-actions/auth v1 composite
  • google-github-actions/setup-gcloud v1 composite
  • google-github-actions/setup-gcloud v0 composite
  • slackapi/slack-github-action v1.19.0 composite
.github/workflows/single_gke_run.yaml actions
  • actions/checkout v2 composite
  • google-github-actions/auth v1 composite
  • google-github-actions/setup-gcloud v1 composite
.github/workflows/test-binary-package-install.yml actions