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CDCgov / seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
https://cdcgov.github.io/seqsender/
Apache License 2.0
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NCBI & GISAID account creation docs #9

Closed nbx0 closed 6 months ago

nbx0 commented 1 year ago

Will be very helpful to have step-by-step instructions with screenshots in the documentation for creating an account, highlighting which fields will then be needed later in seqsender.

dbtara commented 1 year ago

This is s request that came in via NCBI, related to this issue. They have requested that Seqsender direct users to the documentation listed here https://submit.ncbi.nlm.nih.gov/sarscov2/genbank/#ftp-submissions for any account creation so they can contact the correct group. this is the correct url for sra-submissions https://submit.ncbi.nlm.nih.gov/sarscov2/sra/#step6

you only need to request it once though.

dbtara commented 7 months ago

you all really need to update the instructions so that NCBI team can triage the requests the right way. The users are being given the run around at this time

leebrian commented 7 months ago

@dthoward96 would you please provide an estimate for when you can review and address this?

dbtara commented 7 months ago

I did review your updated instructions in the dev branch https://github.com/CDCgov/seqsender/tree/dev?tab=readme-ov-file#prerequisites. but wanted to add that a group account is not the same as center account. you need center account for XML submissions.

dthoward96 commented 7 months ago

@dbtara we've updated the documentation for it now. https://github.com/CDCgov/seqsender?tab=readme-ov-file#prerequisites

dbtara commented 7 months ago

Thank you these look great. I do want to mention that even though you list these account creation as pre requisites, there is still value in this set of scripts to generate submission ready files that can be uploaded manually. You can frame these instructions as prereqs for automated submission. Not sure if the pipeline can stop at generating the files or it will fail w/o these settings

dthoward96 commented 6 months ago

Thank you these look great. I do want to mention that even though you list these account creation as pre requisites, there is still value in this set of scripts to generate submission ready files that can be uploaded manually. You can frame these instructions as prereqs for automated submission. Not sure if the pipeline can stop at generating the files or it will fail w/o these settings

Thanks for the feedback! I've incorporated new documentation in the next version update better explaining how to manually submit data.