v474 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v474 of the UCSC Genome Browser software has now been released.

The main changes are:

• Added setColorWith to allow wiggles to be colored by a bigBed
• Allow people to select Exit Mult-region on the pop-up box
• Better error messages if an assembly hub db isn't found for some reason
• Added a cart rewrite to support moving decipher tracks into a supertrack
• More work on adding support for non-ASCII characters in hgTracks and PDF
• Fixed a subtle drawing bug in zoomed-in bigWigs
• More fixes for hideOthers, make sure that tracks that are on by default are really hidden
• Hide legend if all gnomad pli tracks are hidden
• Suppressed unnecessary error log messages due to loading a hic file with an invalid normalization type
• Add in GENCODE hgc gene and transcript name display in table, as check for HGCN is missing miRNAs not in HGNC but in mirBASE
• Fixed an issue in loading expRatio data when the number of experiments exceeded the number of exons; such files should now be able to be loaded and processed (e.g. for conversion to bigBed)
• Making sure that hgGeneGraph is not spawning more and more dot programs.
• Rework the use of /scratch/tmp /data/tmp and /dev/shm temporary filesystems in the automated pipelines to accommodate new cluster machines
• Fixup security points in the assembly request CGI script that is sending emails
• hgPhyloPlace: add option for subtree JSON files to persist instead of being cleared after 2 days

And data-related changes:

• Updating VGP collection of assemblies in preparation for multiple alignment
• 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.v474.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