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phac-nml / irida

Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
https://irida.ca
Apache License 2.0
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NCBI SRA link is broken in docs #348

Closed tom114 closed 4 years ago

tom114 commented 5 years ago

Describe the bug

Link to NCBI docs to set up bulk SRA uploader is broken. Previously linked to https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Establishing_a_Center_A_

NCBI SRA export configuration - An SRA bulk upload user account must be created with NCBI to allow automated SRA uploads. See NCBI SRA Handbook for details.

Steps to reproduce the problem

What were you doing when you encountered the problem?

  1. Go to https://irida.corefacility.ca/documentation/administrator/web/ page
  2. Click on NCBI SRA Handbook link
  3. 404

Expected behaviour

What did you expect to happen? Go to a page describing bulk upload

Additional context

@tom114 has done some looking into their current docs and I don't see where this section is now located. This bit of docs might need to be revised.

tom114 commented 5 years ago

Closest I can find to the docs is https://www.ncbi.nlm.nih.gov/biosample/docs/submission/faq/ which links to https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/submit/public-docs/, but all the docs folders are empty in there.

tom114 commented 5 years ago

We should as part of this update the docs on how the NCBI uploader works.

apetkau commented 5 years ago

I asked NCBI what happened to these books and was informed that they were out-of-date and were removed.

I believe the expected method to setup such an account is to email NCBI (the SRA support email) directly and ask for a "Center account for simplified format" and that you want to use the FTP (instead of Aspera) method to connect. We should update our docs to reflect this.