a) GATK version used: gatk-18.104.22.168
b) Exact command used: gatk
c) Entire error log: bash: gatk: command not found
I'm trying to run gatk on my university's cluster. I do not have root privileges. Therefore, I need to use conda.
I created the gatk env and installed the package following the instructions here: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4
After activating the environment and running 'gatk' (or 'gatk --help', or 'gatk you-name-it'), I get this error: 'bash: gatk: command not found'
If I test whether the new variant filtering tool (CNNScoreVariants) is working using '
python -c "import vqsr_cnn"' I get the correct output: '
Using TensorFlow backend'. But I cannot get gatk to run anything in my env.
Any ideas what might be happening?
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