v361 Genome Browser Available

[Brian Raney]

Good Evening Genome Browser Mirror Site Operators:

The version v361 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.v361.zip

The version v361 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/v361.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

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v362 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.v362.zip

The version v362 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/

See also: http://genome.ucsc.edu/goldenPath/help/mirror.html

cartDump cartReset das hgApi hgBlat hgCollection hgConvert hgCustom

Thanks, Hiram

[Hiram Clawson]

Good Evening Genome Browser Mirror Site Operators:

The version v363 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.v363.zip

The version v363 CGI binaries can be found at:

http://genecats.soe.ucsc.edu/builds/versions-all/v363.html

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v364 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.v364.zip

The version v364 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/

See also: http://genome.ucsc.edu/goldenPath/help/mirror.html

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

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

April 2018 note: v363 has a new CGI binary: hgCollection
This function is available via the blue bar navigation links:
My Data > Track Collection Builder
This tool allows multiple tracks to be copied and grouped
together into one composite track or "collection". See also:
http://genome.ucsc.edu/goldenPath/newsarch.html#040318

July 2017 note: v351 has a new CGI binary: hgLinkIn

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/v364.html

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v365 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.v365.zip

The version v365 CGI binaries can be found at:

http://genecats.soe.ucsc.edu/builds/versions-all/v365.html

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v366 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.v366.zip

The version v366 CGI binaries can be found at:

http://genecats.soe.ucsc.edu/builds/versions-all/v366.html