v489 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v489 of the UCSC Genome Browser software has now been released.

The main changes in this release are:

• Incoming URLs with an "apiKey" parameter on the URL are skipping the CAPTCHA.
• Visibility fixes to the gear and X icons in hgTracks.
• Added two new glyph types for decorators: + and X.
• Fixed error when VCF tree display is a subtrack of a composite.
• Removed 0-length characters from user search strings.
• Restore tab switching on hgHubConnect being saved to the URL.
• Added support for genePred in quickLift.
• "verbose" variable on the URL is not read from the cart anymore.
• Added -bed option to bigWigToWig to selectively output wiggle regions (contributed by Michael Hiller).
• Introduced a function cartOrCfgOption() that will look in the cart and then in hg.conf for a configuration variable, so we can turn on config variables using manual entry into the cart.

And data-related changes:

• Added HPRCv2 custom chromAlias names to GenArk HPRC assemblies.
• 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.v489.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