Problem: GATK insallation

Question

[whb]

Hi I am new to bioinformatics and programming language. I am having trouble installing GATK following the biostar handbook. After install and register, it gives me error message command gatk not found when entered gatk -help. Hoping someone could help me with this.

I downloaded GATK3.8 from https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef and then untar it by tar xjf GATK3.8-1-0-gf15c1c3ef.tar.bz2 then gatk3-register ~/GATK3.8-1-0-gf15c1c3ef/ and then it says it is copying to the environment but I cannot use it....

Please let me know if more information is needed.

[ATpoint]

Please google what PATH is in an Unix environment and how to add executables to it.

[Nicolas Rosewick]

please use GATK4 not 3.8 : https://software.broadinstitute.org/gatk/download/ . And here is the quick start tutorial from GATK website : https://software.broadinstitute.org/gatk/documentation/quickstart

[steve]

alternatively if you are familiar with conda you can install it that way; https://anaconda.org/bioconda/gatk4

[ddraki2008]

installing with conda worked for me! Thank you Steve! Also indeed one has to be careful to install gatk 4 and not gatk 3.8.