v472 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v472 of the UCSC Genome Browser software has now been released.

The main changes are:

• Added new options to the right-click menu: hide all others, move to top, move to bottom
• Upgraded jQuery and jQuery-ui to the latest versions
• Force all tracks into coverage mode if 32K image size would otherwise be exceeded
• Users can now specify their parallel load timeout value
• Added (i) icons to table browser to better indicate you can mouseover for help text
• The hgLiftOver CGI and the command-line liftOver tool now include an option to keep a copy of the positions from the input file in the lifted output (for formats like BED, genePred, and others that include an item name field or something similar). This should help keep track of which items get mapped where for some users
• Various improvements to both the hgGateway search and new GenArk search
• Amino acid display now only shows up at base level
• Made the two reset genome browser links in the menu the same.
• Performance improvements for Hi-C tracks (and anything else that uses fakeCurl) - we now do a better job of re-using an existing udc handle for a series of requests on the same file. This should also fix some issues associated with having "too many file handles" open when viewing multiple Hi-C files at once
• The option to change some track draw colors is now available on their hgTrackUi page as well as the pop-up configure box in the main browser, and that option remembers what color was previously chosen for that track
• Repair for being unable to change decoration draw modes in the UI (an important variable wasn't being set)
• GBiC now attempts to repair tables it fetches from UCSC's servers before using them
• liftOver and hgLiftOver no longer leave temp files around when lifting coordinates in position format (chr:start-end)
• hgTables identifiers buttons fix - hubs call these functions with a NULL conn, needed to add a check for call with NULL conn identifiers getXrefInfo function
• hgSession backup.c Rocky 9 tar now requires the command line option --exclude before the parameter "."
• GBIB: Fixed MySQL trackDb tables before accessing them (MySQL tables on hgdownload are often in a crashed state)
• Ongoing work on hubtools: make hub.txt given a directory tree with big* files, first try at upload into hub space
• Continuous GenArk process improvements

And data-related changes:

• 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.v472.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