Download from SRA tool inputs
The workflow DownloadFromSRA (long-read-pipelines/DownloadFromSRA/2) requests a column for the SRA ID and a gcs_output_dir. Does this tool require me to use a preexisting GCS bucket? I tried using the gs link, but have been getting the error "
does not have storage.objects.list access to the Google Cloud Storage bucket
If I do not need a preexisting bucket, how do I specify this? The documentation is unclear.
Comments
13 comments
Hi Alex,
Happy to help here. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace (see the icon with the three dots at the top-right)?
1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press Enter on your keyboard
2. Click Save
I'll be happy to take a closer look at how this is currently configured and come back with my recommendation for how to resolve it. Are you supplying a gs link to an external (outside of Terra) bucket you have access to? If so, you may need to give your proxy group address, found in your user profile, to the bucket and supply it with the appropriate permissions. You can read more about that here: https://support.terra.bio/hc/en-us/articles/360031023592-Understanding-and-setting-up-a-proxy-group
Kind regards,
Jason
Thanks Jason. Shared, and I'll try that.
Hi Alex,
Let us know how it goes, and if you would like us to take a closer look at the workspace/configuration, please share a link for the workspace. As it is a group, we don't get individual notifications of being added.
Many thanks,
Jason
Sorry about that, just sent the link
It didn't work, even when I gave it a bucket of its own, and special permissions. Am I missing something?
stderr:
Hi Alex,
To confirm, you added this address found in your profile to the bucket and gave it storage.objects.list access permissions, is that correct?
Kind regards,
Jason
Yes, as well as the pet account from that error, just to be sure
Hi Alex,
Thanks for confirming. Our engineer is seeing that the pet account is in your proxy group, so there shouldn't be issues as far as permissions. I'd like to take a closer look at these jobs. Can you point me to your workspace once again?
Kind regards,
Jason
Sent
Hi Alex,
I was able to run this workflow successfully using a clone of the workspace, and one of my own buckets. I will investigate further to see if I can find out why the result is different.
Kind regards,
Jason
Hi Alex,
I've confirmed I was able to get a successful run by ensuring my proxy group had these permissions. Can you share a screenshot of your permissions for your proxy group to show that you have given it the same? If you haven't, please provide these permissions on your bucket to your group and try running again to see if we get a different result.
Kind regards,
Jason
I had only given it the Creator role, not the Viewer role. Adding both fixed it right up, thanks!
Hi Alex,
Perfect, glad to hear! If we can assist with anything else, please let us know.
Kind regards,
Jason
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