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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.

charlesreid1
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Ruturaj Kulkarni
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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.
Nicole Deflaux
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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

Paul Grosu
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