Docker images
GATK-SV utilizes a set of Docker images for execution within containerized environments.
Publishing and availability
Dockers are automatically built and pushed to the us.gcr.io/broad-dsde-methods/gatk-sv repository under two different conditions:
- Release: upon releasing a new version of GATK-SV. These Dockers are made permanently available.
- Commit: upon merging a new commit to the development branch. These Dockers are ephemeral and may be periodically deleted. Any users needing to preserve access to these Docker images should copy them to their own repository. Also note that these images are built on an "as-needed" basis, meaning an image is only updated if it has been changed in any way by the commit.
The full set of current images are automatically published and pushed to a public Google Artifact Registry and listed in the dockers.json file.
Microsoft Azure mirrors of all images can be found in dockers_azure.json, but these are not currently available for public use.
Regions (IMPORTANT)
Users using Google Compute VMs outside of the us-central1 region, i.e. in other NA regions or continents, must copy all
docker images to a repository hosted in their region. If using a Terra workspace, the region is listed under Cloud Information:Location in the workspace dashboard. Please see
this article
for more information.
Failure to localize Docker images to your region will incur significant egress costs.
Versioning
All Docker images are tagged with a date and version number that must be run with the corresponding version of the
WDLs. The Docker images built with a particular version can be determined from the dockers.json file by checking out
the commit or release of interest and examining dockers.json, e.g.
v0.29-beta.
Note that a given commit may contain a mixture of Docker image version tags if only a subset of images has actually been updated, reflecting the "as-needed" rebuild policy described above.
All Terra workspace releases have the WDLs and Docker images synchronized.
Cloning a Terra workspace copies a snapshot of the current workspace. Any future updates to the original workspace will not be propagated to the clone.
We strongly recommend using a single version of GATK-SV for all projects. Switching versions may lead to batch effects and/or compromise call set fidelity.
Workflow inputs
All GATK-SV WDLs utilize a subset of the Docker images, which are specified as inputs. For example,
the sv_pipeline docker is supplied to the input sv_pipeline_docker in many WDLs.
Builds
An in-depth guide to the GATK-SV Docker system and building Docker images is available in the Advanced section.