Demo of using Cromwell outside of FireCloud
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
data
.gitignore
LICENSE
README.md
align.cloud-inputs.json
align.inputs.json
align.wdl
demo.sh
gcloud2.cfg
google_auth2.json
running_instance.png
storage.png

README.md

Cromwell sans FireCloud

It is possible to use Cromwell outside of FireCloud while still using Google Cloud.

There are lots of instructions on how to do this on Cromwells docs.

pre-requisites

You'll need to download the cromwell jar and install google cloud tools.

You'll also need to have accounts and credentials setup on Google Cloud. Next you'll need to copy the data to Google Cloud. After checking out this project you will need to copy the data over to google cloud. Note the "biofx-demo" is the base of the project.

gsutil cp ./data/reads/small/* gs://biofx-demo/reads/
gsutil cp ./data/ref/small/small/* gs://biofx-demo/ref/

You will also need to create an empty directory in google cloud storage to serve as the base storage for the cloud run. e.g. gs://biofx-demo/run_base.

You'll also need to create a service account with access to Genomics Pipeline as editor.

configuration files

gcloud.cfg is one file you need to edit to describe you're cloud variables. I tried to add some placeholders to highlight the fields which need editing. You will also need to download your google cloud service account credentials. I provided a blacked out version in file google_auth2.json.

You will also need to edit demo.sh to specify the path to your cromwell jar.

running the demo

./demo.sh will run the demo

You will know the cloud version is running by following the logs. You can also log into the google cloud console and you will see the VM started shortly after the cloud run begins (it'll take a minute or so to start typically). example of compute engine console.