CODEWITHSUNDEEP
google-apigoogle-genomicsdockstore
Ruturaj Kulkarni
Ruturaj Kulkarni

Reputation: 1

Does dockstore-tool-samtools-index have GATK/BAM/Chromwell already configured?

Just wanted to know if the docker image with name dockstore-tool-samtools-index which is available here "https://quay.io/repository/cancercollaboratory/dockstore-tool-samtools-index" and given as an input to the Google Genomics API (pipelines.create) contains the genome tools such as GATK/BWA or Cromwell. Any help regarding this will be appreciated.

Thanks.

Upvotes: 0

Views: 72

Answers (2)

Paul Grosu
Paul Grosu

Reputation: 61

One aspect of Docker images is that they usually try to have only one specific tool installed on them. This way the images are kept as small as possible with the idea that they can be used like modules.

There are images listed in the Dockstore search link provided by Nicole above which have BWA installed. Cromwell usually launches Docker containers rather than being installed on a Docker image, since it is more of workflow management system. You are always welcome to create your own custom image with the preferred installed software packages to fit what you need.

Hope it helps,

Paul

Upvotes: 0

Nicole Deflaux
Nicole Deflaux

Reputation: 155

It does not appear to contain those additional tools: https://github.com/CancerCollaboratory/dockstore-tool-samtools-index/blob/master/Dockerfile

Here's how to check:

  1. Find the docker container on https://dockstore.org/search-containers.
  2. Click on the "GitHub" link in the row with the container of interest.
  3. Read the contents of the Dockerfile to see what the image will contain.

Upvotes: 0

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