v491 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v491 of the UCSC Genome Browser software has now been released.

The main changes in this release are:

• Single path for loading bigBeds, and auto-recognizing the bigBed type based on the header.
• Initial import and rework of a new faceted UI for composite tracks, intended for situations where there are too many tracks for the existing composite UI to be usable. The feature was graciously contributed by Andrew Smith at USC.
• Added a checkbox that turns on rearrangement mode automatically for all CTs generated by hgBlat.
• Fixed another jquery-upgrade-induced bug on the composite track UI page.
• Fixed a problem quickLifting between human assemblies.
• Fixed link to hs1 browser from hub management page listing track hub.
• hConnectCentralNoCache can now access remote central servers.
• The right-click menu in hgTracks was listing all visibility options for tracks with an onlyVisibility setting (which is supposed to limit options). It has been made aware of the setting.
• Fixed maf frames caching bug.
• Fixed search bug on assembly hubs with supertracks caused by spurious calls to hubCollectTracks.
• Made listExisting endpoint to hubApi/liftOver respect fromGenome and toGenome arguments, taking precedence over the filter argument. If both fromGenome and toGenome arguments are present, they are ANDed together.
• Explicitly send cookies when doing async cart requests.
• Added option to twoBitMask to allow a bigBed file for masking.
• Fixed mafAddIrows and mafSplit to recognize GenArk GCx... assemblies in MAF files where the problem was the assembly name has dots in the name, and MAF files delineate assembly name and sequence name with a dot.

And data-related changes:

• 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.v491.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