Problems running gatk - gatk: command not found

Question

[michael.flower.14]

I want to install gatk to have a go at using it to variant calling. I've installed it according to package instructions here https://bioconda.github.io/recipes/gatk/README.html

, but get the error that gatk commands aren't found.

1. Install: conda install gatk

2. Register: gatk-register downloaded-stuff

However I get the error: -bash: gatk: command not found

I've read it might work with either of these:

./gatk --help
gatk3 --help

But I still get the same error.

I then thought it could be a path problem, so I added the directory to my path as follows:

export PATH=/Users/michaelflower/opt/anaconda3/pkgs/gatk-3.8-hdfd78af_11/:$PATH
export PATH=/Users/michaelflower/opt/anaconda3/pkgs/gatk-3.8-hdfd78af_11/bin/:$PATH
export PATH=/Users/michaelflower/opt/anaconda3/envs/bioinfo/opt/gatk-3.8/:$PATH
echo $PATH | tr ":" "\n"

/Users/michaelflower/opt/anaconda3/envs/bioinfo/opt/gatk-3.8/
/Users/michaelflower/opt/anaconda3/pkgs/gatk-3.8-hdfd78af_11/bin/
/Users/michaelflower/opt/anaconda3/pkgs/gatk-3.8-hdfd78af_11/
/Users/michaelflower/opt/anaconda3/envs/bioinfo/opt/gatk-3.8/
/Users/michaelflower/opt/anaconda3/pkgs/gatk-3.8-hdfd78af_11/bin
/Users/michaelflower/opt/anaconda3/pkgs/gatk-3.8-hdfd78af_11
/Users/michaelflower/bin
/Users/michaelflower/bin
/Users/michaelflower/opt/anaconda3/envs/bioinfo/bin
/Users/michaelflower/opt/anaconda3/condabin
/Users/michaelflower/bin
/Users/michaelflower/bin
/Library/Frameworks/Python.framework/Versions/3.7/bin
/Library/Frameworks/Python.framework/Versions/2.7/bin
/Library/Frameworks/Python.framework/Versions/3.5/bin
/usr/local/bin
/usr/bin
/bin
/usr/sbin
/sbin
/opt/X11/bin
(bioinfo)

But I still get the error.

Any help would be great, thanks!

[Kevin Blighe]

Unsure what's happening - to where did conda say that it had installed it?; what were the status messages? This may also help: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4

[michael.flower.14]

Thank you, I'm not sure where it installed it. Searching for gatk I found the above locations that I added to my path, but no joy. I tried running conda list, but it just list the package names and not their locations. Any suggestions? Thanks!

[vdauwera]

Have you tried asking for help in the GATK forum? They may be able to help you figure this out. https://gatk.broadinstitute.org/hc/en-us/community/topics