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Last pushed: a month ago
Short Description
Docker image for GA4GHshiny package
Full Description

Docker image for GA4GHshiny package

This Docker image provides the GA4GHshiny Bioconductor package.
GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application.
It also integrates with Beacon Network.
The web application runs on Shiny Server exposing the TCP port 3838.
By default, it connects to Hosting Thousand Genomes Project.

To run this image, execute:

docker container run --detach --name ga4gh-shiny --publish 3838:3838 --rm welliton/ga4gh-shiny

It will be available at http://localhost:3838/.
To stop container run.

docker stop ga4gh-shiny

To change the default GA4GH server endpoint set environment variables:

  • HOST URL of the GA4GH-based server entry point.
  • TXDB Name of the TxDB package (should be none, TxDb.Hsapiens.UCSC.hg19.knownGene or TxDb.Hsapiens.UCSC.hg38.knownGene)
  • ORGDB Name of the OrgDB package (should be none or org.Hs.eg.db)
  • SERVER_NAME Name of the GA4GH server name (should be none or string).
docker run --detach \
  --env HOST=http://1kgenomes.ga4gh.org/ \
  --env TXDB=TxDb.Hsapiens.UCSC.hg19.knownGene \
  --env ORGDB=org.Hs.eg.db \
  --env SERVER_NAME="Hosting Thousand Genomes Project" \
  --name ga4gh-shiny --publish 3838:3838 --rm welliton/ga4gh-shiny

Buiding this image

git clone git@github.com:labbcb/docker-ga4gh-shiny.git
cd docker-ga4gh-shiny/
docker build -t welliton/ga4gh-shiny .

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welliton
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