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I am looking for the file `gatkcondaenv.yml` and could not find anywhere. Could someone please help?

Hi

I am trying to execute the gatk GermlineCNVCaller and I am encountering the below issue:

java.lang.RuntimeException: A required Python package ("gcnvkernel") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.

While it is understood that this command requires gcnvkernel Python package; I am wondering why it is not there in my GATK4.1.2.0 conda environment. I have installed GATK using conda by running the following command:

conda install -c bioconda gatk4

I could see a similar post on the forum where @SkyWarrior has asked to install gatk conda environment mentioned in the README.md which supposedly should be this one. I can also see that the command to install gatk using conda using YML file would be

conda env create -f gatkcondaenv.yml

I am looking for the file gatkcondaenv.yml and could not find anywhere. Could someone please help?

Answers

  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    It should be included in the zip package that you can download from the front page.

  • cnormancnorman United StatesMember, Broadie, Dev ✭✭

    The gatkcondaenv.yml.template file is a template file that is used by the gatk build to create the .yml file that is included with each release. It cannot be used directly. As @SkyWarrior mentioned, the file that should be used is the one included in the .zip file that corresponds to your gatk version.

    I know this is a bit confusing, but the bioconda environment is maintained by the bioconda community, not the GATK team. Although it installs GATK, it does not activate the GATK conda environment that is part of GATK and that is required to run the CNV and CNN tools. The gatkcondaenv.yml does that.

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