v478 Genome Browser Available

[Jonathan Casper]

Good Evening Genome Browser Mirror Site Operators:

Version v478 of the UCSC Genome Browser software has now been released.

Please note: We recently moved our servers to 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:

• Added sort option to bedToBigBed utility.
• Added a cart rewrite for the new Splicing Impact supertrack.
• Explain how to download big* files on the Table Browser schema page.
• Added support for quickLifting mySQL beds, including custom tracks.
• Added ability to turn off table name based handling in CGIs per track will default to type based handling.
• Do not create a hub on invocation of hgCollection. This should reduce number of empty hubs.
• Fixed another prop() vs attr() jquery upgrade bug, this time when turning on subtracks.
• Fixed minor hgTracks imageV2 bug - add one only if we are drawing center labels.
• hgConvert will now report when it's unable to find a chain file instead of crashing (this is very rare).
• GBiB will now update from a frozen binary set until we make it compatible with our new compilation setup.
• sqlTableSize return value switched from int to long type to support tables with more than 2^31 rows.
• Removed sandbox commands from our mariadb table dumps for better compatibility with older mariadb and mysql installations.
• Proof of concept preview of contributed tracks to GenArk hubs working out of /gbdb/ hierarchy.
• Working toward getting GenArk hubs to function out of the /gbdb/ local filesystem.
• Fixed file path security concern in hgEncodeVocab.
• Improvements to wuhCor1 big tree build process.

And data-related changes:

• PubTator track now includes not only SNPs from rsIDs extracted from text, but also other variants discovered by the tmVar2 software from NCBI and grounded to dbSNP IDs.
• Adjusted default track visibilities on GenArk hubs.
• 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.v478.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