Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Alternate way to install GATK4, without using conda or the docker?

ngeraldngerald Member
edited June 21 in Ask the GATK team
I've run GATK4's CNV Detection Utilities on the docker through my local system before. I'm now trying to run it on my server. I followed the instructions on the '(How to) Install and use Conda for GATK4' page but unfortunately my server neither supports docker images nor conda installations.

Is there an another way I can get it running with all dependencies?-
- I already have GATK installed on the server, but I can't run DetermineGermlineContigPloidy, GermlineCNVCaller and ostprocessGermlineCNVCalls without gcnvkernel installed.

- In particular I'm trying to get GATK with gcnvkernel installed


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @ngerald

    Another way you can work around conda and docker is by manually installing all the libraries in gatkPythonPackageArchive.zip that comes with the GATK zip file.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited June 25

    We tried something similar on our end using pip install when we couldn't used docker or conda. Take a look at this shell script: gs://gatk-tutorials/scripts/install_gatk_4110_with_condaenv.sh

Sign In or Register to comment.