v468 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v468 of the UCSC Genome Browser software has now been released.

The main changes are:

• Pop-up hgc pages can now be exited by clicking outside the box.
• Extended DNA case/color output now works for track hubs.
• Increased the font size for jquery dialogs.
• Force underlines under lowercase g in modern web browsers that are too smart for biology.
• PSL custom track default settings now shows mismatches.
• Removed the requirement for defaultIsClosed and Priority from the hub groups setting.
• In some situations, the browser mouseover text was reporting the same exon number for multiple different exons in a track. This is now fixed, and the mouseover text for each exon should accurately reflect its index.
• More tooltip fixups after QA asks revealed original implementation bugs: get item coordinates correctly and setup scroll and mousemove events correctly.
• Continuous GenArk process improvements.

And data-related changes:

• The UCSC Genes track on human genome assemblies has begun marking MANE transcripts in a different color to help identify them. This color is distinct from the ones used to indicate coding/non-coding/etc. in non-MANE transcripts.
• New track PubTator rsIDs under “Variants in Papers” for hg19 and hg38. This track contains dbSNP IDs extracted from titles, abstracts, and PubMed Central full text papers. The dbSNP IDs were curated by PubTator3, an NCBI tool that publishes regular updates.
• New track gnomAD v4.1 on hg38.
• 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.v468.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