denis-yuen/icy-blackberry

Example command line tool for the HCA Hackathon

icy-blackberry

Example for the HCA Hackathon

Usage

Use handy quick start tutorial to setup our dependencies

Run with cwltool

cwltool --non-strict Dockstore.cwl params.cwl.local.json

Run with Cromwell

Download from https://github.com/broadinstitute/cromwell/releases (test with a newer release)

java -jar /home/dyuen/.dockstore/libraries/cromwell-0.21.jar run Dockstore.wdl params.wdl.json

Run with Dockstore (consult launch-with)

Setup permissions for file destinations in Dockstore.json

dockstore tool launch --entry quay.io/denis_yuen/icy-blackberry:1.1 --json params.cwl.local.json
dockstore tool launch --entry quay.io/denis_yuen/icy-blackberry:1.1 --json dockstore.cwl.remote.json

dockstore tool launch --entry quay.io/denis_yuen/icy-blackberry:1.1 --descriptor wdl --json params.wdl.json
dockstore tool launch --entry quay.io/denis_yuen/icy-blackberry:1.1 --descriptor wdl --json params.wdl.json --wdl-output-target s3://oicr.temp