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DivBase v0.1.1

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@RMCrean RMCrean released this 12 Oct 15:13
v0.1.1
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RMCrean Rory Crean
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DivBase is a service built and maintained by SciLifeLab Data Centre that enables life science researchers at Swedish institutions and their collaborators to manage, explore, and query genomic variants in VCF format alongside associated sample metadata.

Notable changes

  • Maximum run times set for user queries. (query tsv: 10 min, query vcf and dimensions update: 10 hours)
  • Prevent multiple queued dimensions update jobs for the same project from entering the queue (to avoid wasted compute).
  • Optimise DivBase for running with multiple workers given that DivBase tasks take a "long time" to run.
  • Documentation has new sections on maximum run times and troubleshooting failed jobs.
  • divbase-cli help text improved for several commands.

Developer tools

  • The admin panel's task_history view now shows task_name.

DivBase server deployment notes

  • Requires a database migration (adds task_name to task_history table).
  • New optional env vars added: SAMPLE_METADATA_TIME_LIMIT_SECONDS, BCFTOOLS_QUERY_TIME_LIMIT_SECONDS, VCF_DIMENSIONS_TIME_LIMIT_SECONDS.
  • Workers configured to take one task at a time, and long/slow tasks use late acks, so a busy worker doesn't hold on to queued jobs when other workers are free.
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