v461 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v461 of the UCSC Genome Browser software has now been released.  Our apologies for the delay; we needed to correct a bug at the last minute (regarding hub performance in hgTracks).  If you have already updated to the v461 files made available earlier this week, you may wish to update again.

The main changes are:

• Add a way to limit RAM used by the browser
• Make exon numbering mouseovers work in squish mode
• Autorecognize the number of fields in bigBed
• Add logging of high water mark of RAM usage
• Beginning again on quickLift with an idea for exported hubs. New words to learn
• Initial prototype experiments on an API findGenome function
• Updated chrM RefSeq annotations on hg38, hg19 and mm39
• Continued additions to GenArk assemblies
• Show hub subtrack shortlabels in the "table" dropdown of the table browser
• Mouseover speed optimization: wait for the actual element to be moused over before creating all the related mouseover node elements
• hash the INFO fields during vcf header parsing so the data parsing afterwards is faster
• Add a "-fieldsIsFile" flag to vcfToBed to read INFO fields to keep from a file instead of the command line
• Spiffy HTML mouseovers in clinvar track (hgTracks' HTML is getting bigger and bigger...)
• Auto-resize hgTracks if user comes in not from hgGateway
• More GBIC changes for Rocky 9 and RHEL based on user feedback
• Adding a "developer mode" to GBIC: You run "browserSetup.sh dev" on a fresh linux server and you get vim and the kent tree installed and can edit and use "make alpha" to build your local mirror from source instead of using the binaries from hgdownload
• Removed hundreds of lines of cruft from common.mk
• Some minimal CIRM DCC (aka SSPsyGene DCC) changes for Parisa/Jim
• Initial version of the "hubMake" tool that generates a hub.txt for files in a directory. Track settings can be adjusted via tracks.ra (manual), tracks.json (good for scripts) or tracks.tab files (good for bulk-changes with awk and cut). move bigBed/bigWig files into subdirectories to create composite tracks. If 80% of bigBed files have a bigWig with the same name, "views" are created

And data-related changes:

• Improvements to wuhCor1 big tree build process.
• Re-do gnomAD v3.1.1 track to a have a cancer vs non-cancer filter, ready for QA

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.v460.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