v469 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v469 of the UCSC Genome Browser software has now been released.

The main changes are:

• Added a configure page option for controlling whether hgc clicks open in pop-ups or not.
• Made knownGene handle like regular tracks by hgSearch, moved HGNC and MANE search results ahead of knownGene in priority.
• Changed some styling of hgSearch search results.
• Hi-C tracks now have support for version 9 of the hic file format (the current latest). Basic support for other normalization modes is also included, but we recommend you add any normalization to all resolutions in the file instead of only selected ones.
• Standardized the font size of our dialog windows (rec. track sets, multi-region, etc).
• Changed chroms to chromAuthority names in hgBlat and hgPcr.
• Track heights now capped at 31,000px.
• Print BLAT version on hgPcr form since ask for it.
• Made priority optional in groups.txt. for the hub groups feature. Also actually sort by priority if specified.
• Fixed defaultIsClosed flag on the hub groups feature and changed it to sort groups by name without regard to case.
• Fixed double call to vfprintf in defaultWarn.
• Added -tsv option to pslMap to output TSVs for mapInfo files rather than autoSql tab format.
• Fixed shortcut for bigWigs not being positional. This was causing a problem on track hubs.
• hgGene will now skip over trying to generate an RNA structure PDF if the corresponding postscript file is missing. To generate postscript files, visit the hgGene details page for that gene.
• hgSession will now only load sessions from URLs that are actually URLs, and no longer reports the content of bad settings (it was a security flaw).
• Rewrote commonNames.pl into commonNames.py to avoid /cluster/home/ NFS overload.
• Working up new data table assemblyList for use in gateway page assembly search and replacement to the fixed html text of the current assembly request page.
• Experimenting with placing the GenArk hub files directly in /gbdb/genark/ to avoid the potentially slow or external single point of failure hgdownload server.
• Continuous GenArk process improvements.

And data-related changes:

• chainNet tracks for hs1.
• 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.v469.zip

or in our Github repository in the "beta" branch and also tagged with the version number.

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