Functionality

jneffjneff BostonMember, Broadie, Moderator admin
edited July 2016 in Archive

Functionality

What are Google buckets and how do they connect with FireCloud?
Google buckets store data in the Google Cloud Platform. Every workspace is attached to a bucket where data is stored and results are written.

Buckets are automatically generated and attached to a workspace whenever a new workspace is created (either through cloning or de novo).

Workspace data model attributes may also reference files in buckets created outside of FireCloud. It is the responsibility of the bucket owner to manage the ACLs on that bucket. Analysis results will always be written back to the bucket attached to the workspace.

If you would like support with setting up a bucket or workspace, please post your question to the FireCloud Forum.

How do I access the bucket that is associated with my workspace?
On the workspace Summary tab, you can click on a link to your bucket. The link will begin with “fc” e.g., fc-098345xx-25aa-47c6-8d52-51c9ea889986d. For more information on buckets, refer to the Workspaces topic in the User Guide.

How can I give FireCloud users access to my data?
You can share your workspaces with any FireCloud user, provided the user has registered, has an activated account, and you know the Gmail address or Google-managed identity that the user provided during registration.

What file types are supported on Firecloud?
FireCloud is agnostic to file types. The required file types are determined by the methods, tools and workflows. Please see FireCloud Tutorials for tool- and workflow-specific inputs and outputs. If you have questions about a specific file type, you can post to the FireCloud Forum.

Does it matter what browser I use with FireCloud?
Although FireCloud may run on any browsers, it will be most stable and functional on Google Chrome.

*How are compute and storage costs charged to FireCloud users?**
Before you can clone or create workspaces, FireCloud administrators must create a FireCloud Billing Project for you or grant you access to an existing FireCloud Billing Project that they created for another user.

All compute and cloud storage costs in FireCloud are tracked through FireCloud Billing Projects, which transmit charges to a Project’s Google Billing Account. When you create or clone a workspace in FireCloud, it is linked to a single FireCloud Billing Project that tracks all storage and compute costs for that workspace.

FireCloud administrators can create a FireCloud Billing Project if you own a Google Billing Account. Steps to set up a Google Billing Account and more information about FireCloud Billing Projects can be found here.

Alternatively, FireCloud administrators can grant you access to an existing FireCloud Billing Project that they created for another user. For example, if you are a member of a lab or program, your principal investigator (PI) or program manager may have requested the creation of a FireCloud Billing Project.

In that case, they would submit a FireCloud Billing Project Request Form requesting to add you to the FireCloud Billing Project. They would need to provide the name of the FireCloud Billing Project and the Gmail address or Google-managed identity you used to register.

Please note that all FireCloud Billing Projects are created by FireCloud administrators and only FireCloud administrators can grant users access to an existing FireCloud Billing Project.

Also, note that if a FireCloud user (collaborator or PI) shares a workspace with you, granting you WRITER access, you can compute within that workspace. All charges incurred for that workspace will be tracked through the workspace’s FireCloud Billing Project and charged to that Project’s Google Billing Account.

Can FireCloud workflow results be visualized?
FireCloud currently supports Nozzle Report integration as in Firebrowse and will soon support the Integrative Genomics Viewer (IGV).

How can I see jobs in progress?
You can view jobs through the workspace Monitor tab. The workspace display screen will also highlight running workspaces in blue.

How can I see if a job has failed and at what stage?
The workspace display screen highlights workspaces in red to indicate failure. You can also view the workspace Monitor tab to view details of the failure.

Does FireCloud send a notification if a job fails?
No. Currently, there are no automatically-generated notifications.
You would need to log-in and check the status on the workspace display screen or workspace Monitor tab. If you click on the Monitor tab, you can view details of the job failure.

What is FireCloud’s workspace data model?
To help you organize your data and results, FireCloud’s workspace data model provides predefined entity types, entity relationships, and entity attributes.

FireCloud Entity Types:

  • participant
  • participant set
  • sample
  • sample set
  • pair
  • pair set

FireCloud’s workspace data model also provides structure for analysis runs by requiring an entity type (e.g., pair set) on which to run an analysis.

Results from data runs can be populated directly to the workspace data model for use in downstream analyses.

For more information, refer to the Data Model section of FireCloud Basics in the User Guide.

Does my data have to live in a Google bucket to be accessible to FireCloud?
Technically yes, although it does not need to live in the Google bucket owned by the workspace. Data copies (both explicit and through workspace cloning) are shallow: references are copied rather than creating new instances of the data objects. This leads to workspaces containing references to data in buckets external to the workspace. Note, however, that the results of any analysis run within a workspace will be written to the bucket attached to the workspace.

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