GATK Installation MS windows 11
Hi, I am trying to install GATK4 on a Windows 11 OS computer. My University only uses windows for our research related tasks. I was tasked with learning and installing this software on our systems. How would I install GATK4 on a windows 11 computer?
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Unfortunately GATK is not supported under Windows operating systems directly. To be able to use GATK in a Windows machine there are 3 possible ways.
1- Use the docker version of GATK. This is a valid option. It requires you to get Docker Desktop installed on your system. However you need to pay attention that file paths under windows are not valid and cannot be used to call files for GATK. Mounted directories must be taken into consideration when providing linux style paths to those files to be consumed by GATK.
2- Using Windows Subsystem for Linux 2 to use GATK. This is another possible way of using it though you need to pay attention to have WSL2 to be installed not WSL1 as WSL1 is not a valid linux environment. File paths need to be revised and regular windows paths may not be used to call files.
3- Using a Linux VM inside Windows via Hyper-V or another hypervisor. This is the ultimate way of using it but it may not be considered an usage of GATK under Windows.
Please pay attention that first 2 methods also mean that you need to have a Hyper-V enclosed virtual machine present in your machine which cannot use all the memory available under Windows and may require additional configuration changes to use close to maximum memory you need to allocate for it.
I hope this helps.
Regards.
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