v353 Genome Browser Available

[Brian Raney]

Good Morning Genome Browser Mirror Site Operators:

The version v353 source is now available at:
http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labeled with version number:
http://hgdownload.soe.ucsc.edu/admin/jksrc.v353.zip

The version v353 CGI binaries can be found at:
rsync -avP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.soe.ucsc.edu/apache/cgi-bin/

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. See also:
https://genome.ucsc.edu/license/

*********************************************************************
***** The genome browser system can be installed on a linux system
NOTE: with the 'GBiC' script (Genome Browser in the Cloud) from
***** the 'Genome Store': https://genome-store.ucsc.edu/
***** See also: https://genome.ucsc.edu/goldenpath/help/gbic.html

***** The genome browser system can be used in a Virtual Box VM
NOTE: image from the 'Genome Store': https://genome-store.ucsc.edu/
***** See also: https://genome.ucsc.edu/goldenPath/help/gbib.html

*********************************************************************

July 2017 note: v351 has a new CGI binary: hgLinkIn which is a feature
under development,
details to follow in later release notes.

June 2017 note: v350 has a new CGI binary: hgGeneGraph with associated files
in cgi-bin/pyLib/ and cgi-bin/loader/dot_static
This binary requires the package python-mysql to be
present on the system.
Example install commands depending upon your system:
yum install MySQL-python
apt-get install python-mysqldb
pip install MySQL-python

February 2017 note: v345 recent htdocs improvements were released for
static html page
style and organization. Please note
htdocs/template.html
for an example static page organization if
your mirror site
has site specific static html pages.
Work has also taken place in CGI binaries to
conform with
Content Security Policy guidelines:
https://www.w3.org/TR/CSP2/

https://developer.mozilla.org/en-US/docs/Web/HTTP/CSP

December 2016 note: v342 new CGI binary now included: hgGtexTrackSettings

October 2016 note: v339 changed name of phyloGif to phyloPng

*********************************************************************

Summaries of changes for this version update can be found here:

http://genecats.soe.ucsc.edu/builds/versions-all/v353.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene
hgGeneGraph hgGenome hgGtexTrackSettings hgHubConnect hgIntegrator hgLiftOver
hgLinkIn hgLogin hgMenubar hgMirror hgNear hgPal hgPcr hgPublicSessions
hgRenderTracks hgSession hgSuggest hgTables hgTrackUi hgTracks
hgUserSuggestion hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloPng


and these configuration files:

/usr/local/apache/cgi-bin/all.joiner
/usr/local/apache/cgi-bin/encode/cv.ra
/usr/local/apache/cgi-bin/extTools.ra
/usr/local/apache/cgi-bin/greatData/*
/usr/local/apache/cgi-bin/hgCgiData/*
/usr/local/apache/cgi-bin/hgGeneData/*
/usr/local/apache/cgi-bin/hgNearData/*
/usr/local/apache/cgi-bin/hgcData/*
/usr/local/apache/cgi-bin/loader/*
/usr/local/apache/cgi-bin/pyLib/*
/usr/local/apache/cgi-bin/visiGeneData/*

Please rsync --delete these directories:

/usr/local/apache/htdocs/js/*
/usr/local/apache/htdocs/style/*

The script in the source tree: src/product/scripts/updateHtml.sh
can be used to update your htdocs directory with the correct delete
operation on /js/ and /style/ directories.

A new hgcentral.sql file is available at:
http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql

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

Thanks, Brian