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.
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.
Notice:
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!
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.
gatkPythonPackageArchive.zip
manolis
Member ✭✭
GATK 4.1.0.0
Just a simple question:
I have to unzip the gatkPythonPackageArchive.zip? Where gatk use it? (germlineCNV?)
Many thanks
Best Answer
-
SkyWarrior
Turkey ✭✭✭
You need to create a conda environment in order to install requirements for those python packages. Some of those requirements are packed into that zip file. Check the README.md file for how to create a gatk conda environment for automated installation.
Answers
You need to create a conda environment in order to install requirements for those python packages. Some of those requirements are packed into that zip file. Check the README.md file for how to create a gatk conda environment for automated installation.
Thank you for the suggestion @SkyWarrior. @manolis that is correct.
As always many thanks @SkyWarrior and gatk team!!!
GATK 4.0.11.0, server no Docker image
Hi, I was looking this page because I had the following warning:
$ source activate gatk
$ source deactivate
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'
if
$ source activate gatk
$ conda deactivate
Seems everything ok
You need just to update your (How to) gatk page?
Many thanks
You may need to ask that to conda developers. This does not seem to be a gatk issue.
I usually use conda activate gatk and conda deactivate. I have not had a single issue for a long time.
Thanks @SkyWarrior