v463 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v463 of the UCSC Genome Browser software has now been released.  There was an issue with the files posted earlier this week, so if you've preemptively grabbed the source code and/or compiled CGIs, you might want to update again.  The issues affected the hgTracks CGI, and caused some problems with the left navigation arrow and hubs that were unreachable.

The main changes are:

• hgSession now has a "view count" column in the session list and a new copy to clipboard button for every session link.
• Added a reset buttons for hgTrackUi filterText text input boxes.
• Made the hgBlat "sequence duplicated" message more human-readable.
• Made maxItemsPossible an hg.conf variable. This variable limits maxItems to be no more than maxItemsPossible.
• Added a link "chrom sizes" to the menu bar, and pushed up the chrom.sizes download instructions on that page.
• Changed bigChain code to look in standard place for the bigBed file holding the links by adding ".link.bb to the end of the bigDataUrl.
• Changed some old code that was allocating a huge amount of memory off the stack to use a static buffer off the heap.
• Workaround: missing pix cart variable triggered page-reload which broke rtracklayer.
• Showing only tables from the db knownGeneVx in TB if user selected a knownGeneVx track.
• Clinvar otto fix: they changed their format for somatic mutations.
• hgPhyloPlace: support for larger pathogen genomes e.g. M. tuberculosis and arbitrary metadata.
• Continuous GenArk process improvements.

And data-related changes:

• bigDbSnp files should now go into coverage mode using the summary levels when their item load fails.
• dbSnp153 rebuild to correct formatting issue on hg19.
• 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.v463.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