v464 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v464 of the UCSC Genome Browser software has now been released.

The main changes are:

• Track hubs can now designate their own track groups.
• Made clicks from hgTracks to hgc open in a dialog so the user stays on hgTracks.
• Tooltip improvements: made the timeout for the next tooltip a little slower and fixed a positioning bug.
• Fixed the arrow buttons, but this time hopefully without breaking the entire site.
• Added back the link with hub info to track hub in blue bar.
• Improved exon mouseover as per Ana and user ML.
• Added option -asOut to bigBedInfo to output the autoSql only for reuse.
• Combined MGC and ORFeome into a super track on hg38, hg19, and mm10.
• For bigBed labels, if there's only one choice, just ask the user if they want them or off.
• Fixed a problem with session numbers being printed out as signed integers instead of unsigned.
• Small optimizations to hgSearch html printing.
• Continuous GenArk process improvements.

And data-related changes:

• 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.v464.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