v467 Genome Browser Available

[Jonathan Casper]

Good Morning Genome Browser Mirror Site Operators:

Version v467 of the UCSC Genome Browser software has now been released.

The main changes are:

• Removed some of the text below the hgTracks image.
• Made some tooltips have longer delays than others and removed some of the less helpful tooltips.
• hgc page for BAM: removed the "English" CIGAR text and added a new legend for normal cigar string.
• Added endpoint to the API: genarkGenomes - to list the GenArk genome assemblies or test if one exists, remains to be documented.
• Added support in the API for bigChain, bigMaf and bigDbSnp track types, remains to be documented.
• Added new API function -revComp to the get sequence complement (reverse).
• bigBedInfo now outputs the no. of defined fields.
• Added hg.conf option to load a mirror-specific .js file (for china mirror).
• Made the hgTracks basic tutorial on by default and documented the hg.conf parameter.
• hg.conf option to switch on itemRgb by default.
• hg.conf option to remove the dink left/right buttons under the image.
• Added option for overlapSelect statistics output to have a TSV header on output.
• Added chainToBigChain command.
• Added pslToChain -fixStrand option to correct negative target strands rather than abort or ignore psl.
• Fixed decoding of chain scores in hgc, which is a double in the data structures; it still displays as an int in hgc.
• errAbort instead of SEGV when bigPsl alignment table is not found. Unsure why this happened, but at least this removes the white screen of death. Included a note about periods in track names that can cause failure.
• Include track name in some of the filter error messages so we can have a clue about what to fix.
• lib/vcf.c: fix bug in parsing of END keyword when not defined in the VCF header.
• Continuous GenArk process improvements.

And data-related changes:

• gnomAD missense and pli v4.1 tracks ready for QA.
• NMD decorators on knownGene for hg38.
• 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.v467.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