v471 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v471 of the UCSC Genome Browser software has now been released.

The main changes are:

• Changed track control labels so they word-wrap.
• For assembly hubs, strip hub_ prefix in table browser fasta output.
• Made hgTrackUi schema links visible in the window, even when a subtrack config is open. Limit the subtrack config to the size of the window, but make it scrollable.
• Improved genbank search by reducing the number of MySQL commands.
• Allow configuration of bigBed filters on bigGenePred tracks.
• Fixed a few instances of '.' in table names not being allowed/anticipated.
• Committed the first draft of a simple "hubtools" command line tool, which makes hub.txt given big* files.
• AssemblySearch with API findGenome function nearing completion.
• GenArk assembly collection for: BRC - Bioinformatics Research Center nearing public release (https://hgdownload.soe.ucsc.edu/hubs/BRC/).
• Continuous GenArk process improvements.

And data-related changes:

• Added VSV accessions to ClinVar track.
• 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.v471.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