v485 Genome Browser Available

[Jonathan Casper]

Good Afternoon Genome Browser Mirror Site Operators:

Version v485 of the UCSC Genome Browser software has now been released.

Please note: our utilities and CGIs now have an extra dependency on libcurl  If you do not already have libcurl installed on your system (it's often already there), then you will be unable to use this latest release until you add it.

The main changes in this release are:

• Added table browser support for bedMethyl.
• Added the ability for hgConvert and hgLiftOver to use GenArk hubs.
• Better error message when barchart trackdb definition is wrong.
• Removed CAPTCHA from hgRenderTracks.
• Removed CAPTCHA from hgSession.
• Fixed erroneous code in vcfTrack.c when parallelFetch.threads=0.
• Allow hubspace data directory to exist on a filesystem where realpath will fail, because the location stored in hgcentral does not match what hgwX is seeing, as long as we have the data directory prefix in hg.conf.
• Added botdelay to hgFileSearch.

And data-related changes:

• Bionano track for hg19 and hg38.
• mGap track for rheMac10.
• HPRC 464 assemblies now available in GenArk.
• Updated GenArk with all RefSeq 'reference' assemblies. Now including over 700 'archaea' assemblies and over 20,000 bacterial assemblies in GenArk.
• 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.v485.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

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

Version v487 of the UCSC Genome Browser software has now been released.

Please note: our utilities and CGIs now have an extra dependency on
libcurl If you do not already have libcurl installed on your system (it's
often already there), then you will be unable to use this latest release
until you add it.

The main changes in this release are:

- toolTips now line break correctly
- barChart SVG drawing code is now in javaScript for better use of
- client web browser features
- hubSpace continued development
- better support for GEO URL-encoded links with more informative
- usage message
- Improved the hgConvert and hgLiftOver functions on GenArk hubs.
- Adjust CAPTCHA behavior on hgTables
- Improve the column names for single cell output using combined
- facets and matrix, changed column count to cell count, and column
- val to read count. Also added a new optional tag for trackDb
- singleCellColumnNames off to support old default column names

And data-related changes:

- Panmask track for hg38.
- Mexico Biobank track for hg38
- GenArk assembly count over 45,000 assemblies:
- https://hgdownload.soe.ucsc.edu/hubs/

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.v487.zip

or in our Github repository release that is tagged with the version number:

https://github.com/ucscGenomeBrowser/kent/releases

Beware of fake scam web sites offering up genome browser software downloads.

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.

Hiram Clawson
UC Santa Cruz Genomics Institute