freeseek / mocha

MOsaic CHromosomal Alterations (MoChA) caller
MIT License
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Question regarding setting up MoCha on Google Cloud #10

Closed xuj18 closed 3 years ago

xuj18 commented 3 years ago

Hi Giulio, Thanks for this well documented WDL pipeline! I am trying to set up my Google VM to run MoCha. And I followed your suggestions up to the step for starting the Cromwell server on the Google VM: "(java -Xmx3500m -Dconfig.file=PAPIv2.conf -jar cromwell-58.jar server &)". However, I got the error message as below -

Google Pipelines API configuration is not valid: Errors: google configuration stanza does not contain an auth named '123456789876-compute@developer.gserviceaccount.com'. Known auth names: application-default google configuration stanza does not contain an auth named '123456789876-compute@developer.gserviceaccount.com'. Known auth names: application-default

Do you know how I can fix this?

Thanks! Jiayi

freeseek commented 3 years ago

After you included the stanza:

google {
  application-name = "cromwell"
  auths = [
    {
      name = "service-account"
      scheme = "service_account"
      json-file = "{google-project}.key.json"
    }
  ]
}

You have to change both auth = "application-default" occurrences to auth = "service-account".

I am not sure what your error means but it would be much more effective for me to provide help if I could see how you have actually edited the PAPIv2.conf file. Unfortunately this is a tedious technical step that has to be endured if you want to run your own Cromwell server.

xuj18 commented 3 years ago

Hi Giulio, Yes I changed the name, scheme, and two places for auth to the specific service account. Please see attached for my PAPIv2.conf file. Thanks so much for your help!

Best, Jiayi


From: Giulio Genovese notifications@github.com Sent: Monday, March 8, 2021 12:28 PM To: freeseek/mocha mocha@noreply.github.com Cc: Xu, Jiayi jiayi.xu@mssm.edu; Author author@noreply.github.com Subject: Re: [freeseek/mocha] Question regarding setting up MoCha on Google Cloud (#10)

USE CAUTION: External Message.

After you included the stanza:

google { application-name = "cromwell" auths = [ { name = "service-account" scheme = "service_account" json-file = "{google-project}.key.json" } ] }

You have to change both auth = "application-default" occurrences to auth = "service-account".

I am not sure what your error means but it would be much more effective for me to provide help if I could see how you have actually edited the PAPIv2.conf file. Unfortunately this is a tedious technical step that has to be endured if you want to run your own Cromwell server.

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