This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Problem: GATK insallation

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
• 4,684 views • link
updated by ddraki2008 • ddraki2008 • written by whb • whb

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

• 0 views • link
written by ATpoint ATpoint

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.

• 0 views • link
written by ddraki2008 • ddraki2008

0 answers

No answers yet.

Log in to answer this question.

More posts like this