v476 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v476 of the UCSC Genome Browser software has now been released.

Please note: This is the last release that will be compiled on CentOS 7.  We are migrating our environments to Rocky Linux 9.5 going forward.  We plan to maintain this release in a separate directory on our download server in the future for legacy mirror servers, and to continue building 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.

The main changes in this release are:

• Feature ‘Right click > hide other tracks’ and ‘hide’ now hide the parent instead of the last child. This means that you can no longer have tracks in the track list that have no subtracks shown.
• First major commit of hubspace.
• Update browserSetup.sh after running it on Rocky 9.5 in vm on hgwdev.
• Fix for https cert locations on Ubuntu/Debian, and updated https whitelist with a fresh scan of last year's log of the RR and official mirrors.
• Various fixes to address compiling on the new Rocky 9 OS.
• Edge and Safari have a 32k cart string size limit. We now work around that.
• Fixed code that chops strings so as not to call ArraySize with NULL.
• Ported hgBeacon to python3.
• Make sure jquery library is included in iframes for hubCheck on the hub development tab.
• Work on making HAL build-compatible.
• Add a version of stringify (stringifyEz) that is in an interpreted language so it does not have to be built first and in the path. Useful if building just parts of the tree.
• Fixing issues in the source tree for the transition to newer linux version, more static libraries, fewer dynamic libraries.
• Preparations are underway to host all of the GenArk assembly hubs in the /gbdb/ hierarchy to eliminate the dependency on hgdownload service.
• Fixed up crash bug in findMotif program when missing arguments.
• Improvements to wuhCor1 big tree build process.

And data-related changes:

• (New) - cytoBand track from NCBI to mouse/mm39.
• (New) - CIViC database track for cancer variant interpretation on hg19, hg38. The track will be updated monthly.
• Renamed various conservation tracks and docs pages to make them easier to use, now that we have so many of them. E.g. ‘Conservation’ into ‘UCSC 100 Vertebrates’.
• Fixed hg19 REVEL track mouseover text.
• 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.v476.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