Beginner query - why dbGap

Hello, still a newbie to Gen3 and with a rather obvious question - why is it that when you are setting up a program, you have to use a dbgap id? Must the data already be deposited in dbGap for a successful Gen3 setup?

thanks for your assistance.

Hi @Lavinia!

No, there is no such requirement.

Our developers mentioned that dbgap_accession_number is hardcoded in a few places so developers do not advice to rename this field it in the dictionary. You can use any value for this field for your datasets.

@Lavinia, I wonder if you are interested in our gen3_community slack channel, where people share their experience in setting up Gen3?

Thanks Viktorija, I appreciate the fast response!

Hmm, I am having trouble setting up a program and project. I get a success message when setting up a project, but when I got to "submit", I cannot see my project listed under "List of Projects". I'll have another read through the documents and see if I have missed anything. Should I get a green success message when setting up a program?

Hi Viktorija,

Sorry, also meant to say that I am interested in the Slack channel thanks!

with regards,

Lavinia.

Maybe some permissions are missing in the user.yaml file for your new program and project? Here is a link for latest user.yaml Guide fence/user.yaml_guide.md at master · uc-cdis/fence · GitHub

Great! We will send you an invite!

The invite to gen3_community slack sent :slight_smile:

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