Install GATK version 4.1.0.0 using Conda.

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dongju

• August 29, 2023 08:32

Thank you for providing this great program.

I have encountered an issue while trying to install GATK version 4.1.0.0 in a virtual environment using Conda, and I would like to inquire about it.

 

unzip gatk-4.1.0.0.zip
cd gatk-4.1.0.0
conda env create -n gatk -f gatkcondaenv.yml

Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound: 
  - tk==8.5.18=0
  - setuptools==36.4.0=py36_1
  - certifi==2016.2.28=py36_0
  - readline==6.2=2

I have encountered this error.

I would appreciate any advice you can provide.

Thank you

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• 

  Gökalp Çelik

  • August 29, 2023 14:59
  • Edited

  Hi dongju

  Since GATK 4.1.0.0 is an earlier version conda dependencies might have changed and some of the dependencies are even not available in the conda repository. Can you try installing a recent version of GATK like 4.3.0.0 or 4.4.0.0?

  Here is the versions of setuptools as an example from the conda repository. And as you can see 36.4 is not there anymore. You may still use the docker version of 4.1.0.0 which already has all the conda environment dependencies installed properly. 

  

  Another solution would be to modify the yml file to point to the conda-forge channel for packages but this would be totally experimental and unsupported. Any non-matching package version installed might cause errors or calculation differences among tools. Our actual suggestion would still be using the latest GATK 4.4.0.0 version or the docker version of 4.1.0.0. 

  I hope this helps. 

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  dongju

  • August 30, 2023 02:00

  Thank you for the helpful response. I have installed GATK version 4.4.

  Now, I want to use GATK CreateSomaticPanelOfNormals with multiple VCF files as input.

  How can I use the -V option to achieve this?

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  Gökalp Çelik

  • August 30, 2023 05:30

  Hi dongju

  A sample workflow is explained here in the following link. You need to combine your variants into a GenomicsDB format and use that as an input if you have multiple vcf files for your PoN. 

  https://gatk.broadinstitute.org/hc/en-us/articles/13832769396635-CreateSomaticPanelOfNormals-BETA- 

  I hope this helps. 

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  dongju

  • August 30, 2023 05:36

  I appreciate your time:)

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