dsub and Datalab?

[slagelwa]

Today when I was showing a intern how to use dsub they asked me if it was possible to use it in datalabs. That made me stop and think for a minute, and wonder. They said they tried and it wasn't working. I don't see why it won't/couldn't and got to thinking that might be pretty useful. So I though I'd throw it out here and see if anyone else has tried.

[mbookman]

Hi @slagelwa!

I know that people have run dsub from Cloud Datalab, but context matters. A notable thing is when running it on GCE, you need to have launched your VM with proper authorization scopes for calling the genomics API.

It may also matter that when running Datalab on GCE, the VM and hence notebook would be running with the privileges of a Compute Engine service account, so the service account needs to have the ability to call the genomics API.

Hope this helps.

[slagelwa]

Helps a bunch, I'll pass on the bit about privileges.

On Wed, Oct 17, 2018 at 10:27 AM Matt Bookman notifications@github.com wrote:

Hi @slagelwa https://github.com/slagelwa!

I know that people have run dsub from Cloud Datalab, but context matters. A notable thing is when running it on GCE, you need to have launched your VM with proper authorization scopes https://cloud.google.com/genomics/reference/rest/v2alpha1/pipelines/run#authorization-scopes for calling the genomics API.

It may also matter that when running Datalab on GCE, the VM and hence notebook would be running with the privileges of a Compute Engine service account, so the service account needs to have the ability to call the genomics API.

Hope this helps.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DataBiosphere/dsub/issues/128#issuecomment-430717165, or mute the thread https://github.com/notifications/unsubscribe-auth/AKBQyEUsN7B_4IKfA71WO9eEhRuzreC2ks5ul2iIgaJpZM4Xi8kq .

[slagelwa]

Just passing this along

It turns out I just had to install dsub on a datalab cell and it worked!