v481 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v481 of the UCSC Genome Browser software has now been released.

Please note: We are continuing to build our command-line utilities in a more general environment for ease of use, but those binaries rely on a more recent version of GLIBC.  Due to several requests, we have created a one-time set of frozen binaries using an older GLIBC, which may be suitable for users with older systems.  These binaries can be found on our download server at https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v479/.

The main changes in this release are:

• Fixed VCF does not work on extended case-color options in Get DNA for vcf, vcfTabix, and vcfPhasedTrio in hgc.
• Fixed instructions in hgCustom for URL-only custom tracks.
• Fixed broken html generation in hgTrackUi filterBy's.
• Made configuration instructions for URL-only custom tracks more obvious with red message at the top.
• Fixed mangled composite track UI when score filtering is disabled. This caused form and table begin/end mismatches. Also a little bit of movement of some inconsistent code to make it easier to understand where score fitler config is called.
• Added two new accessibility fonts.
• Fixed Table Browser filter error caused by not handling special case of tables with both db table and bigGenePred or bigBed.
• Fixed missing uri encoding in url for ajax callback in track collections js.
• hgVai: fixed corner case (insertion containing stop codon).
• Improvements to hgcentralTidy.c to better clean out hgcentral spam entries.
• Added botDelay to hgNear as a highly executed CGI on RR.
• Improvements to wuhCor1 big tree build process.

And data-related changes:

• 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.v481.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