IMPORTANT: This is the legacy GATK documentation. This information is only valid until Dec 31st 2019. For latest documentation and forum click
here
created by KateN
on 2018-03-12
Notebooks are a Beta feature in FireCloud. As such, they are subject to several important limitations.
Workspace cloning does not copy notebooks
- Currently cloning a workspace does not copy the notebooks stored in the workspace. We are actively working on implementing this, so stay tuned.
- A cluster is yours and yours alone. No one else can view or access your notebook (a project manager can delete it but not open it). The reason for this is security: we store your Google credentials on the Google VM, which cannot be shared with other users.
- Collaboration can occur by sharing notebook files, but not clusters.
Accessing non-FireCloud managed resources
- You can access any FireCloud-managed resources (like buckets) from within a notebook using any standard gcloud client. There is no need to login from your notebook, you are already authenticated. However to access non-FireCloud managed resources from within a notebook, you will need to grant your FireCloud proxy group access to that resource.
- We currently support Python 2, Python 3, and R kernels, all including Spark.
- Our current version of Hail uses Python 3.
- If you have two kernels running at once, you may see slowdowns, try to have only one running at a time.
Updated on 2019-01-22