v482 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators (apologies for the delay, I was out sick!):

Version v482 of the UCSC Genome Browser software has now been released.

While we have not finished updating our GBiB tool to make use of the most recent CGIs, our Docker setup (https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions) has been brought up to date and should now work with these CGIs.

The main changes in this release are:

• Change the hubConnect page so it no longer redirects.
• Improving mouseover of genePred tracks, adding hint to zoom in more to show cDNA positions, and a link to a new doc html page that explains what we mean by "phase 0/1/2".
• Added right-click Track Description feature in hgTracks.js.
• BAM tracks now go into coverage mode if maxItems is exceeded. Also added a cap to the number of items that will be loaded (BAMMaxItems).
• It is now assumed that the RGB value in the ninth field of a bed should be treated as a color.
• Allow .bigBed file extension to work with featureBits.
• Fixed hgBlat table of alignments not available once browsing. This fixes both native blat track and ct blat track.
• Changes to our bottleneck system to better recognize and penalize heavy bot activity on our servers.
• Anti-bot work: wait for 10 seconds on. Added hg.conf that triggers apache log entry when a user arrives without cookies, and added bytedance bot to robots.txt.
• New tool tabToBed: give it a .tsv file and it will guess what the fields with chrom, start, end, name, or give it the names of these fields and it will make an .as file and a .bed file to make a bigBed from the .tsv.
• GBIC changes: a few small changes for OSX, adding freetype for all linuxes, fix straw.cpp for new g++, allow builds on the beta tag when not on the beta branch for mirrors, always use mariadb and removing mysql_config dependency, removing udr, always install curl just in case, redoing the whole Dockerfile using newer commands, address the root user problem for mariadb, and other changes.
• Fixed buffer overflow in fixed-size mouseover buffer by making it a bigger fixed size.
• "hubtools up" no longer re-uploads a file into Hubspace if it's already there.
• hgVai: fixed corner cases surfaced by running vai.pl on EVA snps (40 assemblies, 909M variants).
• Improvements to wuhCor1 big tree build process.

And data-related changes:

• MaveDB heatmap track for hg38.
• Adding "unusual conservation" track.
• Adam Sieoel's LINSIGHT track to hg19 constraint superTrack.
• NMD Escape track for hg38.
• Added triangle decorator to ClinVar track.
• Fixing a panelApp bug in our otto script, CNV and STR panels were missing.
• Minor updates (such as adding gene name to the mouseover) to the Varaico track, which contains literature-extracted variants.
• 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.v482.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