v473 Genome Browser Available

[Jonathan Casper]

Good Evening Genome Browser Mirror Site Operators:

Version v473 of the UCSC Genome Browser software has now been released.

The main changes are:

• Fix density mode for vcfTabix.
• Fix problem with hubUrl being trashed if Genark hub was specified as db.
• Ongoing work on behaving rationally when certain limits are exceeded in hgTracks.
• Primer3 outlink from hgGene now gets +-200bp flanking seq around the first and last exon to design primers around the exons.
• Fix freeType and Postscript handling to deal with UTF-8 encoded strings.
• Adapting the tutorial reminder to say where users can find the tutorial if they click it away now.
• Right click - move to top respects the ruler track.
• Click OK when "enter" key is pressed on trackUi dialog box.
• Now we just filter all the types, like BLATs guess, which makes them consistent and correct, the same as the default behavior it always had.
• The configuration page for some track types can include a selector to change the track color, but the selectors for subtracks of a composite were all being placed in the configuration block of the first subtrack. They are now distributed among the subtracks.
• Don't show download link to big* files on the table browser for non-distribution tracks.
• Fixed jQuery upgrade bugs: group drag and drop of tracks, drop-down checklist position, checkboxes marked as change during a form submit.
• Disable the "download track data in window" option on GBiBs since they don't have an API available.
• More work on right-click - hide all other tracks.
• Continuous GenArk process improvements.

And data-related changes:

• Added NCBI link-outs on NCBI RefSeq gene tracks
• 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.v473.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