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  1. Docker

Running Docker with Swiss Army Knife

PreviousCreating Docker SnapshotsNextPortals

Last updated 8 months ago

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Here is the overview of

To use an gatk image (made in previous sections) with the Swiss Army Knife tool, you will do the following:

Command Line

dx run app-swiss-army-knife -iimage_file="gatk.tar.gz" -iin="data/mock.vcf" -icmd="gatk SelectVariants -V mock.vcf -O selected.snp.vcf –select-type-to-include "SNP""

From there, this will be what the command line prompts will be:

From there, you will see the job log of the Swiss Army Knife App.

Resources

To create a support ticket if there are technical issues:

  1. Go to the Help header (same section where Projects and Tools are) inside the platform

  2. Select "Contact Support"

  3. Fill in the Subject and Message to submit a support ticket.

Full Documentation
Swiss Army Knife