v466 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v466 of the UCSC Genome Browser software has now been released.

The main changes are:

• Added the number of start/end hard and soft clipped bases to the BAM hgc page.
• Plug trackDbCache into hgc and hgTrackUi.
• Skip BAM details if the read is very long.
• Added a new baseView track type that will draw something like the base position track given a set of coordinates from a bigBed file.
• Removed the click & drag to scroll tooltip from hgTracks image.
• Changed "Reset filters" label to "Clear filters" on bigBeds tracks and decorators, as that is really what the button does.
• Fixed native assemblies not being selectable in hgGateway autocomplete.
• Search results in hgTables now bold properly.
• Unify the different color pickers (drag select highlights, track item highlights and track item colors) into hui.js. Ensure the text box and palette selector work.
• Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search.
• Changed hgTracks view DNA link to not have the hgsid twice.
• Skip screen width auto-detection if hgTracks is run from the command line.
• Merged blatHuge implementation. This adds a gfServer and blat that search genomes greater than 4 gigabases.
• Moving to jsdelivr as the CDN as the bootstrap one is slowing us down, we should stop using CDNs altogether.
• Added pslSpliceJunctions to gather information in splice junctions for comparative mapping analysis.
• Improved dbDbToHubTxt.c to allow the creation of a curated track hub instead of just a curated assembly hub.
• Added a script refSeqOnGenBank.py to translate RefSeq genes to the corresponding GenBank assembly.
• Continuous GenArk process improvements.
• New lib module mmHash (memory-mapped hash) for very large lookup tables.
• Util tabToMmHash to make mmHash file from tab-separated file.
• hgPhyloPlace:
• Use mmHash to speed up name/ID lookups and metadata lookups.
• New config option anchorSamples: always include certain samples in subtrees.

And data-related changes:

• HGMD 2023 update.
• Improvements to wuhCor1 big tree build process.
• Continuous GenArk updates and liftOver file generation.

For a comprehensive list of changes for this version, please visit/bookmark (you may need to force refresh in your web browser to see an updated page): https://genecats.gi.ucsc.edu/builds/versions.html

We typically release a new version every three weeks. A summary of all past releases and changes can be found at the above link.

The new source code tree is available at:

https://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labeled with version number at:

https://hgdownload.soe.ucsc.edu/admin/jksrc.v466.zip

or in our Github repository in the "beta" branch and also tagged with the version number.

If you use the GBiB virtual machine with auto-updates enabled, it will automatically update itself on Sunday. If you have installed your UCSC Genome Browser server with the GBiC installation script browserSetup.sh, then you can upgrade it with the command "sudo bash browserSetup.sh update".

If you have installed your Genome Browser manually:

• You can use the following rsync command to copy the CGI binaries into the cgi-bin directory of your Apache server: rsync -avP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
• We provide a shell script to update the htdocs directory, htdocs and cgi-bin must be updated together: https://github.com/ucscGenomeBrowser/kent/blob/master/src/product/scripts/updateHtml.sh
• The hgcentral database contains our curated list of public track hubs and pointers to BLAT servers per database and should be updated regularly. We have released a new MySQL dump of this database: https://hgdownload.soe.ucsc.edu/admin/hgcentral.sql

A license is required for commercial download and/or installation of the Genome Browser binaries and source code. No license is needed for academic, nonprofit, and personal use. More information on our licensing page:

http://genome.ucsc.edu/license/

If you have any questions or concerns, please feel free to write back to this genome-mirror mail list.

Jonathan Casper

UCSC Genomics Institute