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hadasvolk / CompLabNGS

Computational Lab in Next Generation Sequencing and Genomics Data Analysis - TAU 0411358701
MIT License
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Ex6- installing GATK #3

Closed shovalsegal closed 4 months ago

shovalsegal commented 5 months ago

I'm having trouble installing GATK, this is what i did:

  1. downloaded GATK from their website, put it in my repository and extracted the zip fie.
  2. tried to change the PATH in the ".bashrc" file and run the command "gatk- register". that didn't work.

also tried to download the gatk via conda. that didn't worked either.

so i would appreciate some help on how to install gatk.

hadasvolk commented 5 months ago

Hi,

Are you working on an HPC/cluster or your own linux machine? Have you tried to install gatk using conda?

conda create -n gatk -c bioconda gatk

If you are working on an HPC system you might have gatk already avilable for you on the module system.

If you prefer to download and install gatk manually you should make sure you have all needed dependencies installed, e.g. java and perl. You should follow the instructions in the gatk website and forum for detailed troubleshooting and generating a registration codes

shovalsegal commented 5 months ago

I'm working on my own Linux machine, following this instructions https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices. where all the programs should be downloaded to? and regarding to updating the PATH, it supposed to reach the main folder or a sub folder?

hadasvolk commented 5 months ago

You are free to download software wherever you want. Usually it is a good practice to have a dedicated place for all your tools.

Your PATH should contain the full path to directory holding the binary https://linuxize.com/post/how-to-add-directory-to-path-in-linux/