v460 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v460 of the UCSC Genome Browser software has now been released.

The main changes are:

• Save the last 5 searched terms into the autocomplete dropdown
• Big based tracks now go straight into density coverage instead of lowering visibility on item overflow or exceeding height
• Fixed mouseover event not re-raising after the mouseover timer completes
• Fixed bug with tracks not updating when zooming out
• Added a note to longLabel if a VCF track is in coverage mode
• Added hg.conf variable to trust trackDb and not check for data presence at startup
• Exons now show the phase of the first and last codon on mouseover
• Added a menu entry "find short exact DNA match" to the "genome browser" menu
• Added a new button "highlight" and a menu entry to the UI, the same as the "h+m" keyboard shortcut
• The hgBlat "sequence too short" error message now points to our help docs, Hiram's findMotifs tools, and oligoMatch track
• Summary modes now used in bigBeds for coverage mode
• Decoupled item limits for bigBeds from item limits in the display
• Limit VCF fetch to 10,000 items instead of unlimited
• Make the tutorial warning go away if it has been viewed more than 5 times without being explicitly closed
• When submitting the track search form, don't send an empty hubUrl setting as it confuses the cart code
• Fixed up seg fault when doing mrna singlePos searching
• Fixed bug where csv output on Table Browser header was still tsv
• If you add '&verbose=x' to any URL, the CGI will now output the verbose() messages. This means that you can see what UDC is doing. Does not stay in the cart. Feedback by engineers is appreciated.
• Added an alpha option to the clinvar otto track, so I can change the otto track with less risk of breaking the real otto job. This creates a "ClinVar ALPHA" track, so on hgwdev we now have two Clinvar tracks.
• Added more defenses against bots targeting poor hgGeneGraph: a captcha that asks users questions about genomics and higher bottleneck penalties.
• Ongoing GBIC work, new linux distributions came out, partially based on Jorge's feedback, as he used GBIC for the new genome-asia.
• Modified gff3ToGenePred to try hard to find meaningful names for records that don't have a Name attribute.

And data-related changes:

• Clinvar track now has HTML mouseovers, with spiffy bolded text
• Improved GenArk build system to better handle large genomes over 4Gb in size
• Added T2T primate assemblies to GenArk.
• Added European mistletoe assembly to GenArk, large assembly over 90 Gb.
• Continuous GenArk updates and liftOver file generation.
• Improvements to wuhCor1 big tree build process.

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.v460.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