Utilities for Cromwell Hackathon

Clone this repo

cd ~
git clone https://github.com/wleepang/cromwell-hackathon.git

Containers

Build all the containers

cd ~/cromwell-hackathon
./scripts/build

Compiler

Compiles cromwell.jar from source.

Usage

Use the container to build cromwell

cd ~/cromwell-hackathon
git clone https://github.com/broadinstitute/cromwell.git

# this should just build cromwell
# equivalent to `sbt "project server" assembly`
./scripts/compile

If successful, the above should create a cromwell-*-SNAP.jar in the current folder and symlink it as cromwell.jar. On a c5.18xlarge instance this takes about 140-200s.

Runner

Runs the cromwell server locally

Usage

Use the container to run cromwell in server mode

cd ~/cromwell-hackathon/
./scripts/cromwell

This will create a cromwell server on your local machine preconfigured to usse the Batch environment for the hackathon.

You can access the server at: http://localhost:8000/

and either use a web-browser and the SwaggerUI or curl to submit workflows to it.