v477 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v477 of the UCSC Genome Browser software has now been released.

Please note: This is the first release that has been compiled on Rocky Linux 9.5.  A copy of the last CGI release compiled on CentOS 7 is preserved on our download server as "cgi-bin.v476" for rsync and ftp access.  We are continuing to build our command-line utilities in a more general environment for ease of use.

Please also note: The GBiB virtual machine has been migrated to Ubuntu 18.04 LTS.  This migration will not automatically take place on deployed GBiB installations, but newly downloaded copies will be on 18.04.  As this OS version isn't immediately compatible with the newly compiled CGIs, we have frozen CGI updates on GBiB until we have finished our planned upgrades to the GBiB system (i.e. beyond 18.04 to a currently-supported Ubuntu version).

The main changes in this release are:

• Filename now used as custom track shortLabel when uploading a custom track, rather than "User supplied data".
• hgTrackUi and composites: set parent to pack if a child is un-hidden, set children to pack if parent is un-hidden.
• Fixed ClinVar coloring for CNVs.
• Compile user download on Ubuntu using standard static where possible using Docker.
• Add very old program tabFmt to tree due to popular demand.
• Started using a new version of RepeatMasker (v4.1.7-p1) and a new version of windowMasker (v28.0.11) for GenArk browser build.
• Improved source tree build using more static libraries, fewer dynamic libraries: libz.a libm.a.
• 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.v477.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