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

ngeraldngerald Member
edited June 2019 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 2019

    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

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