v479 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v479 of the UCSC Genome Browser software has now been released.

Please note: We are continuing to build our command-line utilities in a more general environment for ease of use, but those binaries rely on a more recent version of GLIBC.  Due to several requests, we have created a one-time set of frozen binaries using an older GLIBC, which may be suitable for users with older systems.  These binaries can be found on our download server at https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v479/.

Please also note: The GBiB virtual machine has been migrated to Ubuntu 18.04 LTS.  This migration will not automatically take place on deployed GBiB installations, but newly downloaded copies will be on 18.04.  As this OS version isn't immediately compatible with the newly compiled CGIs, we have frozen CGI updates on GBiB until we have finished our planned upgrades to the GBiB system (i.e. beyond 18.04 to a currently-supported Ubuntu version).

The main changes in this release are:

• Added support for DropBox for hubs and custom tracks using byteranges.
• Added "view conversions" link to hgLiftOver output page to display conversions as html.
• hgSearch now uses chromAlias.
• First version of a positional heatmap track display that uses several extra fields in a bigBed. This is similar to the existing microarray track type, but should be more flexible (and supports multiple heatmaps in the same track).
• hubCheck now checks that subtracks have the same group setting as their parent to enforce implicit group correctness when the group setting is not set at the right level.
• Added the db parameter to async hgTracks image updates to band-aid the multiple tabs with different genomes but same hgsid confusion.
• hubApi can detect if the genome argument is an assembly hub.
• hubApi getData endpoint can detect if requested tracks are in a track hub and retrieve them without explicitly setting hubUrl argument.
• Increased the number of split tables allowed.
• Improvements to wuhCor1 big tree build process.

And data-related changes:

• Updating GenArk build procedure for NCBI RefSeq track to get proper GeneID values into the bigGenePred file and subsequent proper out links to NCBI gene resources.
• 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.v479.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