v438

Code changes:

• Added a hack to support knownGene in table browser until we get bigBed support for linked fields (#30067)
• Made urlLabel setting support variable substitutions allowing for custom labels and added $ substitution support in bigBarChart (#29954). Chris
• bigSnp tracks can now go into density coverage mode. Brian
• Added a 'custom' naming scheme to the chromAlias to manage incoming sequence names that do not follow standard patterns such as the TOGA tracks (#29982). Hiram
• Added 'copy link' function to gateway description page on GenArk hubs. Hiram
• Cleaned up some more of the buttons on hgTracks (#29676). Max
• Fixed bug with copy to clipboard button on hgSessions (#29583). Max
• Additional words now allowed after "type bigGenePred" in trackDb. Brian
• Disabled parallel loading for interact tracks as it is not thread safe (#30114). Brian
• Increased the size of the buffer that reads in the default cart. Brian
• hg.conf now defaults to using "public" if there is no "curatedHubPrefix" present (#29811). Brian
• Cgi processing of assembly requests is now safer (#28930). Hiram
• Adjusted the lastz/chain/net processing to work with curated hubs (#29819). Hiram
• Added an option to hgLoadOut to accept input for the fa.out file from local file or from URL (#29819). Hiram
• Fixed fuseCsvFields to support multiple tables. Galt
• Cleaned up sqlSafef V2 including cdwWebBrowse and cdwMakeFileTags. Galt
• Fixed minor issues in facet code. Galt
• Ongoing monkeypox enhancements and bug fixes in hgPhyloPlace. Angie

Data changes:

• deCODE and 1k genomes genetic maps track from the 2019 paper ("recombination rate" is our track name) on hg38 (#30044). Max
• Recombination rate track on SARS-CoV-2 published by Angie et al in Science last month (#30074). Max
• Transcriptomic stage track on monkeypox (#30074). Max
• Sequencing primers track for monkeypox (#30012). Max
• UK Biobank / deCODE depletion score track for hg38 from the 2022 Nature paper (#30070). Max
• panelApp track and ottomatization for hg38 (#25568). Max
• Genbank alignments track for monkeypox (#30111). Max
• Turned on dynamic blat service for mpxvRivers genome. Hiram
• Ongoing improvements to wuhCor1 big tree build process. Angie