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.
I am looking for the file `gatkcondaenv.yml` and could not find anywhere. Could someone please help?
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 GATK22.214.171.124 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?