v470 Genome Browser Available

[Brian Raney]

Good Afternoon Genome Browser Mirror Site Operators:

Version v470 of the UCSC Genome Browser software has now been released.

The main changes are:

• Basic support for multiple decorators on one track is in place; documentation (and UI review) pending
• Added checkbox to hgTrackUi of ruler track to make amino acid display more on by default.
• Small doc change on Table Browser intersect page to promote Data Integrator and CLI tools.
• If a track hub has a track specified with a group that is not defined, put the track in the generic group for that hub, not in "other".
• Allow bigInteract tracks' endsVisible to be set via trackDb in addition to hgTrackUi .
• Decorator UI should now respect trackDb settings for blockMode and glyphMode .
• Fixed up mouseOver wiggle track when a track in wiggle mode switches to not wiggle mode, do not display the mouseOver
• knownGene builds will now examine and link to NCBI's RefSeq track instead of our (discontinued) in-house mapping.
• Fixed a bug where an automatic switch to density mode was not setting the track type to wig .
• Suppress mysql freeform query fields in table browser for bigBed, but not knownGene .
• Fixed a problem in the bigBed library with summary levels failing on very large chromosomes.
• Added a cart rewrite for the move to gnomadVariants4 .
• Added resolvPrefix hg.conf option for URL rewrites: when udc URL matches a prefix, then a shell script can be run to get the final URL.
• Fixed an issue where the newly-introduced fakeCurl library had a namespace collision with libcurl, which broke remote halSnake tracks .
• Support added for multiple filterBy sets on the same page of HTML.
• hic files in alternate gbdb locations weren't being found; this has been fixed with a call to hReplaceGbdb.
• 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.v470.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.

Brian Raney

UCSC Genomics Institute