v483 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v483 of the UCSC Genome Browser software has now been released.

Please note: our utilities and CGIs now have an extra dependency on libcurl  If you do not already have libcurl installed on your system (it's often already there), then you will be unable to use this latest release until you add it.

The main changes in this release are:

• Added new bedMethyl track type.
• Added Cloudflare captcha for the entire website on cookie-less access.
• Improved tooltips for genePred tracks with a link to a new docs page.
• Made hgGateway output the cookie headers.
• Fixed "jump to exon" and "jump to codon" to work on bigGenePreds on assembly hubs.
• Searching public hubs is now the default for advanced hgTracks search.
• Fixed "screen grek" problem on composites with dense subtracks by shrinking the font.
• Fixed clinvar otto track and job: adding lolly archive and lolly check, make BED name field unique for decorators.
• Fixed broken 'view sizes' links on GenArk hubs from the gateway page.
• Fixed right-click -> hide others bug.
• Do not look for genome chrom names/sizes in a database when it is a GenArk hub.
• The bottleneck service will now validate that client-supplied hgsids conform to the expected format before using them as a target for usage penalties.
• Merged in simplifyBlatAlwaysCreateCT. Uses ajax and hg.conf setting.
• Removed CDN links to shepherd javascript library which we use for the tutorials.
• Make hgApi use the cart to allow the right-click options.
• Fixed bug where we pthread_detach'd off the end of the array of threads.
• Improvements to wuhCor1 big tree build process.

And data-related changes:

• Added triangle decorators to the ClinVar SNV track.
• Mutscore track for hg19 and hg38.
• M-Cap track for hg19.
• UCNEbase in the "unusual conservation" superTrack.
• 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.v483.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