conda: command not found: gatk.

Question

[bestone]

Hello everyone, I have a problem with Gatk. I downloaded it to my Mac but it has not worked.

First: I created an environment: conda create -n mynev and then I check my env list it. I activated it : conda activate my env. after that, I downloaded the Gatk conda install gatk. however, when i run the Gatk it says command not found: gatk.

Could you pls help me with this issue?

[Pierre Lindenbaum]

how about all your previous questions ? take a time to validate the good answers (green mark on the left). CNNScoreVariants Error ; gatk Hardfilter Error ; samtools install error ; SnpEff Error ; Seqtk ; gff3 file format ; bowtie2 ; BWA- SAM tools alignment default parameters ; FastQC quality ;

[bestone]

I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install the current gatk again, but now gatk is not working at all

[Pierre Lindenbaum]

how about all your previous questions ? take a time to validate the good answers

[bestone]

oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. could you pls with this issue?

[GenoMax]

Follow directions provided by GATK project: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4

[bestone]

Actually, I tried all the steps in this link but it still didn't work. I have anaconda3 on my laptop. Unfortunately, the codes on this site did not work.

[bestone]

Is there anyone who can help me with this?

[666billgaytes]

Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.