Dockstore
GRAPE supports execution from the Dockstore, which is a free and open source platform for sharing reusable and scalable analytical tools and workflows. It’s developed by the Cancer Genome Collaboratory and implements GA4GH Tool Registry Service API (TRS).
To deploy GRAPE from the Dockstore:
Clone the GRAPE repository.
Download reference datasets.
There are four available options:
# Download minimal reference datasets from public available sources (without phasing and imputation)
dockstore tool launch --local-entry workflows/reference/cwl/ref_min.cwl --json workflows/reference/cwl/config.json --script
# Download complete reference datasets from public available sources (for phasing and imputation)
dockstore tool launch --local-entry workflows/reference/cwl/ref.cwl --json workflows/reference/cwl/config.json --script
# Download minimal reference datasets as bundle from (without phasing and imputation)
dockstore tool launch --local-entry workflows/bundle/cwl/bundle_min.cwl --json workflows/reference/bundle/config.json --script
# Download complete reference datasets as bundle from (for phasing and imputation)
dockstore tool launch --local-entry workflows/bundle/cwl/bundle.cwl --json workflows/reference/bundle/config.json --script
4. Run the preprocessing.
dockstore tool launch --local-entry workflows/preprocess2/cwl/preprocess.cwl --json workflows/preprocess2/cwl/config.json --script
5. Run the relatedness inference workflow.
dockstore tool launch --local-entry workflows/find/cwl/find.cwl --json workflows/find/cwl/config.json --script
Each pipeline step requires config.json.
Each config has predefined directories and paths, but you can override these paths by changing them in these files.
Also notice that Dockstore saves its runtime in datastore directory. This directory will grow up with each run. We recommend to clean it up after each step, especially after reference downloading.