v492 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v492 of the UCSC Genome Browser software has now been released.

The main changes in this release are:

• Save HGVS searches onto the search history stack.
• HGVS searches use the refSeqSelect table if the transcript is present.
• Do HGVS searches in the auto-suggest position box on hgTracks.
• Fixed hgTrackUi to properly show filters for bigBeds with less than five fields.
• In bigBed click handling, changed error to warning when trackDb type field count differs from the bigBed header.
• Removed the info link for quickLift groups in hgTracks.
• Fixed gene alleles section of hgGene when doing hgGene in the popup on hgTracks.
• Fixed hgTracks tooltips to store the tooltip information in the 'data-tooltip' attribute instead of in the 'title' attribute to preserve the title strings. wait until DOMContentLoaded to actually parse the titles into 'data-tooltip' so the text size variable is present.
• Fixed default hidden sections in hgGene to properly open when clicked, and fixed the population button in the Common Gene Haplotype Alleles section.
• Fixed PDF output problem in hgTracks. Previously, we had set hgFindMatches = NULL for PDF output to suppress the item search highlight in the generated PDF. But track loading code in bigBedTrack and squishPackyMode both depend on that search term, those routines that need the original search value.
• Added hgTables Summary and intersection buttons for knownCanonical.
• Fixed missing field descriptions for mm39 knownGene.
• Fixed Table Browser to allow bigGenePred to be used like genePred and provide CDS FASTA output.
• Fixed hgTables Sequence output with CDS casing bug that caused introns to be upper case and has existed since 2002.
• Fixed hgLiftOver min match filter with -multiple fixed. It has been allowing too-small regions in the output. Error was in the system since 2013.
• Beginning to import the TOGA V2 annotations. Added a 'hideToggle' class element to hgc description page to allow hide/show of text on the description page for a track item. Function is on the TOGA V2 details page.

And data-related changes:

• 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.v492.zip

or in our Github repository release that is tagged with the version number (https://github.com/ucscGenomeBrowser/kent/releases).

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