Question: Problem: GATK insallation
0
gravatar for chicku
5 months ago by
chicku0
chicku0 wrote:

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.

gatk • 277 views
ADD COMMENTlink written 5 months ago by chicku0
1

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

ADD REPLYlink written 5 months ago by ATpoint28k

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

ADD REPLYlink modified 5 months ago • written 5 months ago by Nicolas Rosewick8.6k

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

ADD REPLYlink written 5 months ago by steve2.4k
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