How to install GATK for command line?

Question

[DdogBoss]

I am running a Snakemake pipeline on a cluster, but am having trouble with GATK.

The error that I am running into is:

Error in rule gatk_register:
jobid: 46
input: /net/dunham/vol1/home/dennig2/yevo_pipeline/workflow/envs/src/GenomeAnalysisTK-3.7-0-gcfedb67.tar.bz2
output: /net/dunham/vol1/home/dennig2/yevo_pipeline/data/pipelineoutput/05_gatk/gatk_3.7_registered.txt
conda-env: /net/dunham/vol1/home/dennig2/.snakemake/conda/82f61b1b43a83fa5851b5687321ca2bf_
shell:
    gatk-register /net/dunham/vol1/home/dennig2/yevo_pipeline/workflow/envs/src/GenomeAnalysisTK-3.7-0-gcfedb67.tar.bz2 > /net/dunham/vol1/home/dennig2/yevo_pipeline/data/pipelineoutput/05_gatk/gatk_3.7_registered.txt
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

I have tried installing gatk and gatk4 through conda into the conda environment, but that doesn't seem to be recognized as a bash command. What is the best way to install gatk for command line on a Linux kernel?

Answer 1

[Istvan Albert]

I have recently installed gatk4 on linux with a conda with

mamba install gatk4

and worked with no problems, what is the problem you are running into (besides Snakemake errors, because who knows what is in those)

I suspect the snakemake workflow is outdated.

[DdogBoss]

I did as you suggested to install the package, and the package was already installed in the environment. I am trying to run this rule:

rule gatk_register:
input:
    f'/net/dunham/vol1/home/dennig2/yevo_pipeline/workflow/envs/src/GenomeAnalysisTK-3.7-0-gcfedb67.tar.bz2'
output:
    f'{OUTPUT_DIR}/05_gatk/gatk_3.7_registered.txt'     
conda:
    'envs/main.yml'
shell:
    "gatk-register {input} > {output}"

I tried running the shell command by itself outside of the pipeline, and came into this error:

-bash: gatk-register: command not found

[Istvan Albert]

you don't need to register gatk anymore, it runs just fine without registering, probably that's why it does not even have that command

[DdogBoss]

You're right. I removed the gatk register, and it is running now. Thanks.