v488 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v488 of the UCSC Genome Browser software has now been released.

The main changes in this release are:

• Added a search bar to the track hub definition documentation page.
• Adding "c h" shortcut to hgTracks to quick-connect a track hub.
• Adding a "hide all" button in the group blue bar.
• Make it obvious to users that identifiers, filters, and intersections have been created and will affect the table browser output using color.
• Remove 0-length characters from input when searching on hgGateway,hgTracks, and hgSearch.
• Fixed bug where we didn’t find normalization options for hic files that don't annotate the first chromosome.
• Have gff3ToGenePred indicate which GFF3 errors can be optionally treated as warnings.
• Show proper links to download server for BAM files on the format description page.
• Correct display of gene name on RefSeq gene track items.
• Fixed problem with lrg track nextExon using the wrong handler.
• Fixed bigBeds limitWiggle optimization to work properly with multi-region.
• Upgrading our NodeJS on dev from 0.10 to version 22, after 12 years.
• Upgraded RepeatMasker process to version 4.2.1 and RepeatModeler process to version 2.0.7. New genome assemblies going forward will use these new versions.
• Ongoing work on quickLift.

And data-related changes:

• Wild-type SpliceAI scores for hg38.
• Added over 3,000 new fungi assemblies to the GenArk collection for the BRC project.
• 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.v488.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