v465 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v465 of the UCSC Genome Browser software has now been released.

The main changes are:

• Allow hubs to declare their own track groups.
• Added a new bigBed trackDb setting for highlighting items, specified the same way as trackDb filters.
• Added a filter on filterBy (dropdown filters) to hgTrackUi.
• Genark hubs can be selected by using db=GC* in trackDb.
• Added 'in new tab' link to hgBlat output page and an info icon to the "make custom track" BLAT button.
• Allow n. notation in HGVS parser.
• Get Genark genomes into hgGateway species auto-complete search.
• Chevrons are no longer drawn in squish mode even if intronGap is set.
• Fixed hgGateway autocomplete to not show nulls for assembly hub hits.
• Made drag selects not open hgc pages.
• Changed exon mouseover after user feedback.
• Tweaked category names when searching for assemblies on hgGateway.
• Skip super long CIGARs on hgc page so the page doesn't crash anymore on long reads.
• Strip off hub_#_ when sending Genark hub data to Galaxy.
• Added an option to bigWigAverageOverBed to output TSV headers.
• Allow a mirror-specific piece of javascript added through hg.conf, can be used for the China mirror.
• hgPhyloPlace: Selected pathogen can now be a group of references and trees, e.g. just "Dengue" for all four types.
• Continuous GenArk process improvements.

And data-related changes:

• New knownGene track for hg19 after more than a decade.
• Changed labeling of HPRC rearrangement track.
• Reorganize chain track composite trackDb entries on GenArk assemblies.
• Added liftOver chain alignment tracks to all primates and mammal GenArk genomes
• 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.v465.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