[genome-mirror] v448 Genome Browser Available

[Christopher Lee]

Good Afternoon Genome Browser Mirror Site Operators:

Version v448 of the UCSC Genome Browser software has now been
released. My apologies for not sending this email for v447.

The main changes are:
- new API endpoint: /list/files?genome=someGenome to provide a list of
download files for the specified genome
- Users can now keep multiple isPCR results in one track rather than
overwriting the custom track with each new hit
- GBiC patch to fix mysql tables that are in a broken state on
hgdownload, like GBIB
- bigMaf is now supported for sequence logos

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:
http://hgdownload.soe.ucsc.edu/admin/jksrc.zip
or labeled with version number at:
http://hgdownload.soe.ucsc.edu/admin/jksrc.v448.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:
http://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.

ChrisL
UCSC Genomics Institute