v484 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v484 of the UCSC Genome Browser software has now been released.

Please note: our utilities and CGIs now have an extra dependency on libcurl  If you do not already have libcurl installed on your system (it's often already there), then you will be unable to use this latest release until you add it.

The main changes in this release are:

• Added support for a new track type: bedMethyl. This format is optimized for displaying methylation information coming from PacBio and Nanopore.
• Show locus name on BLAT results table.
• Simplified the tooltip code to fix lingering tooltip bugs: using a mouseenter and mouseleave event on each item, combined with a timer, instead of the old mouseover + document.mousemove system and multiple timers.
• Require users to have a valid cookie before using hgGeneGraph.
• TLC for the PDF page, removed EPS text and replaced with a note about vector graphics.
• hubspace: The pre-create hook sets the upload path that the rest of the hooks and tusd itself use, so we don't have to move files around anymore.
• Fixed right-click option jump to exon/codon to work on bigGenePreds.
• Removed duplicated link on hgc page on bigGenePred.
• Table browser now shows a "too big" warning when gnomAD tracks are selected.
• Fixed bug when clearing filters on hgTrackUi to reset the actual select.
• Fixed clade option not working in hgCustom.
• Output BAM alignment type in hgc page.
• Fixed multi-region issue with hideEmptySubtracks to correctly use counts of all windows, not just the first.
• Allow alternative namedSessionDb tables when a session was not found, one step towards "universal sessions".
• When our JavaScript code queues cart events and creates a URL, don't double-encode values that are already encoded.
• XSS prevention in error message output for errAbort().
• Allowing a pipe character rather than the dot in MAF files.
• libcurl has been added to the list of dynamic dependencies for our tools, including our otherwise statically-compiled binaries.
• Clinvar otto improvements: added ClinVar lollies to the archive, added a validation to the ClinVar sub lollies script.
• Allow userAgents to circumvent CAPTCHA, defined in hg.conf.private (#35938). Max
• Fixed parasol packet overflow issue in paraNode resurrect.
• Fixed parasol so paraNodeStart passes the name in cluster.ms to pass to paraNode as explicit hostname, and make resurrect and checkJob work correctly.
• Improvements to wuhCor1 big tree build process.

And data-related changes:

• M-CAP track for hg38.
• MutScore track for hg19 and hg38.
• 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.v484.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