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GATK version check failed

I have installed GATK using command - wget https://github.com/broadinstitute/gatk/releases/download/4.5.0.0/gatk-4.5.0.0.zip

then unzipped - unzip gatk-4.5.0.0.zip

checked installation using commnad - gatk --version

But failed.

error

 Command 'gatk' not found, did you mean:
  command 'gate' from snap gate (9.3)
  command 'gitk' from deb gitk (1:2.34.1-1ubuntu1.10)
  command 'gawk' from deb gawk (1:5.1.0-1ubuntu0.1)
See 'snap info <snapname>' for additional versions.

How to check successfull installation? Thanks

gatk bash unix
• 1,732 views • link
updated by GenoMax GenoMax • written by Tundup • Tundup

Either you add the GATK folder to your PATH variable or you need to provide the path to your GATK executable.

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written by DBScan • DBScan

1 answer

You have downloaded and unpacked the source archive, but you haven't "installed" the software. In the case of GATK, the "installation" process is simply extracting the archive into some location and adding the location of the gatk wrapper to your PATH variable. See the documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4 , Section 5.

The gatk command is essentially just a wrapper script for a Java program. If you install the Bioconda package gatk4 with conda install -c bioconda gatk4 you will get version 4.4.0 instead, but everything will be put in place.

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written by Michael Dondrup Michael Dondrup

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