GATK version check failed

Question

[Tundup]

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

[DBScan]

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

Answer 1

[Michael]

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.