Problems running gatk - gatk: command not found

0

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!


vcf


bam


gatk

• 21 views



Source link