WBConfCall 2023.04.20-Agenda and Minutes

Agenda and Minutes

New 18 C. elegans wild isolate genomes from Cristian Riccio

• Sarah sent an email with details on 28th of March to Paul, Todd and Scott.
• Still awaiting response - do we want these as tier 3 or as SVs wrt N2?
• Should these be rendered in JBrowse 2?
• Todd: What would happen to this data going forward into the Alliance? If this data won't be supported at the Alliance, it may not be the long term solution the authors are looking for.

Help Desk

• Please double-check any tickets assigned to you and close, if you can
  • My script is using downloads.wormbase.org - Todd replied; will leave open for now in case there's more follow up
  • Hello, could you please reference.... - I'm leaving this open as a reminder to follow-up with Ranjana and Valerio about references for automated descriptions
  • {"readyState": 4,"requestURL": "/rest/widget/variation/WBVar00543472/molecular_details","status": 500,"statusText": "Internal Server Error"} - there are three similar tickets for this issue. Paolo replied on one, but I'm leaving them open in case there's still work to do.
  • The search directory on the top right.... - request to help with search behavior. Todd, Scott, and Paolo have commented.

Links to Alliance

• Chris spreadsheet for All Hands face 2 face for places to link WormBase to the Alliance, even before trying to embed Alliance widgets. Chris can coordinate with web team. Will add link here later. Will make sure OICR is aware
• Spreadsheet here: https://docs.google.com/spreadsheets/d/1BbZOddok3ktosgWd2FSIy24wky22ldZXfqS-93blvuA/edit?usp=sharing
• New WB GitHub tickets here:
  • https://github.com/WormBase/website/issues/9004
  • https://github.com/WormBase/website/issues/9005
  • https://github.com/WormBase/website/issues/9006
  • https://github.com/WormBase/website/issues/9007

IWM Meeting

• Planning for the WB workshop; anything to discuss?

AWS credentials

• WB needs Genes from nameserver, which is on AWS, so need creds or AMI ?
  • TH
    • I will give a post-mortem of the recent credential leak at the next conference call.
    • The preferred and recommended way to do this would be via an assumed role, not dedicated AWS CLI credentials.
    • I think you mean instance? AMIs are images of instances. IMHO a stand-alone instance is overkill, and already have instances available to run a cron.
  • Juancarlos
    • That's great. I don't know much about AWS. If you're able to set up a cronjob to daily
      • java -cp wb-names-export.jar clojure.main -m wormbase.names.export gene genes.csv
    • And put the output genes.csv somewhere web accessible, I think that's all Caltech would need.
    • I don't know much more about it, other than Matt Russell told me to run that (we went back and forth a bunch of times before it worked).
    • Here's a copy of the .jar file
      • https://tazendra.caltech.edu/~azurebrd/var/work/todd/wb-names-export.jar
    • Also
      • export WB_DB_URI="datomic:ddb://us-east-1/WSNames/wormbase"
    • And .jar was originally at
      • aws s3 cp s3://wormbase/names/exporter/wb-names-export.jar wb-names-export.jar
  • Thanks, JC! We can make that work from one of our persistent instances. I will look when I return from vacation.