I am running GATK4 via docker to run HaplotypeCaller in my Mac OS terminal.
I have connected the docker to my files as follows
*$ docker run -v /Users/imac/Documents/NA12878/myproject:/gatk/myfile -it broadinstitute/gatk:184.108.40.206
then run the Haplotype caller via the gatk in the docker.
(gatk) myfile # HaplotypeCaller -R ref.fa -I file1_mrkdup.bam -O file1_variant2.vcf*
However when I leave the system, the docker container disconnects .Any help will be appreciated. Do we have an alternative version of caffeinate in docker Any help would be appreciated.