[genome-mirror] v441 Genome Browser Available

[Christopher Lee]

Good Morning Genome Browser Mirror Site Operators:

Version v441 of the UCSC Genome Browser software has now been released. This is our last software release of 2022.

The main changes are:

- "return to current position" button on hgCustom

- new HI-C inversion option

- perform a chromosome name lookup asynchronously before doing a full search

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.v441.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.
- 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.

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.

If you have any questions or concerns, please feel free to write back
to this genome-mirror mail list.

ChrisL
UCSC Genomics Institute