SequenceServer BLAST 2.2 release notes

We’re ecstatic to release SequenceServer 2.2.0.

This further builds on some of the great new features and bug-fixes from 2.1.0. Notably:

• Quick as a Lightning Bolt! SequenceServer now launches much faster. This comes from two changes. First, we now only check for databases that need formatting when we intend to format GitHub. And you can now also supercharge your launch time even more when using the new --optimistic flag. This disables all checking and thus should only be done when the administrator is certain that all databases were formatted with appropriate makeblastdb parameters. Combined, our launch times on large databases have reduced from minutes to seconds. Thank you @tadast
• Download large text-format BLAST results without rendering. Sometimes users would run analyses that provided very large results (e.g., BLAST output of 250Mb or more). This can happen when, for example a user runs BLAST from a new geneset containing 10-15,000 genes against a large database, and requests hundreds of hits per query. Showing the result page would typically lead the browser (and sometimes SequenceServer) to crash. We now instead provide a warning, and allow the user to simply download the .xml or tab-delimited BLAST report. Thank you @tadast
  
• Format .faa. We now ensure that SequenceServer also recognizes and formats .faa files (this extension is occasionally used for FASTA files that contain amino-acid sequence). Github
• Error reporting. We now ensure that when database formatting fails, we keep track of errors. Credit @tadast GitHub
• Docker bump. Docker build is now from ruby:3.2.2-bullseye rather than slim-buster. This improves compatibility. Github - thank you @nathanweeks
• Architectural rewiring - some tweaks improve code maintainability

Stay grounded with this supercharged release. All improvements listed above are open source.

Several additional improvements are accessible to users of SequenceServer Cloud BLAST.

Full list of changes:

• Improve test coverage by @Lazy-poet in https://github.com/wurmlab/sequenceserver/pull/657
• Use full image for builder stage; update to bullseye by @nathanweeks in https://github.com/wurmlab/sequenceserver/pull/675
• Fix thread shutdown logic by @tadast in https://github.com/wurmlab/sequenceserver/pull/681
• Handling large BLAST results by @tadast in https://github.com/wurmlab/sequenceserver/pull/682
• Record makeblastdb errors for debugging purposes by @tadast in https://github.com/wurmlab/sequenceserver/pull/683
• Add .faa as a recognised fasta extension by @tadast in https://github.com/wurmlab/sequenceserver/pull/684
• [Performance] Do not perform unnecessary operations in makeblastdb by @tadast in https://github.com/wurmlab/sequenceserver/pull/686
• [Performance] Add –optimistic flag that skips DB checks by @tadast in https://github.com/wurmlab/sequenceserver/pull/687
• Gh actions grg by @augeas in https://github.com/wurmlab/sequenceserver/pull/688

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