v458 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v459 of the UCSC Genome Browser software has now been released.

The main changes are:

• Added a search bar to the home page
• longLabel is now updated when maxWindowCoverage is active and format is BED4-8
• When CGIs running on RR or euro/asia-node cannot connect to hgcentral they now output a long email message with contact email address.
• Support for Google Analytics 4
• Last mouseover now re-triggers event that fired while we were blocking when a tootlip was already visible
• Small tweaks to hgSearch display
• Small bug fix to bigBed extra fields display after a user complaint.
• Test now runs in parallel using make -j.
• Added hg.conf variable (trustTrackDb) to force the CGI's to validate trackDb instead of just trusting it.
• Ongoing work on hgGeneGraph against bots
• Continuous GenArk process improvements

And data-related changes:

• Continuous GenArk updates and liftOver file generation
• Improvements to wuhCor1 big tree build process

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.v459.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