Entering edit mode
21 months ago
michael.flower.14 ▴ 170
I want to install gatk to have a go at using it to variant calling. I've installed it according to package instructions here
, but get the error that gatk commands aren't found.
conda install gatk
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!
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
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!
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