v339 Genome Browser Available

[Brian Raney]

Good Morning Genome Browser Mirror Site Operators:

The version v339 source is now available at:
http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with version number:
http://hgdownload.soe.ucsc.edu/admin/jksrc.v339.zip

The version v339 CGI binaries can be found at:
rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

Please note description of new features in this release and history of features:

http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features#4_October_2016.2C_v339

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:
http://genome.ucsc.edu/license/

*********************************************************************
October 2016 note: v339 changed name of phyloGif to phyloPng

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

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

Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene
hgGenome hgHubConnect hgIntegrator hgLiftOver 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/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.cse.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 v340 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with version number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v340.zip

The version v340 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

Please note description of new features in this release and history of features:

http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features#25_October_2016.2C_v340

Thanks, Hiram

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v341 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with version number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v341.zip

The version v341 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

Please note description of new features in this release and history of features:

http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features#15_Nov_2016.2C_v341

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v342 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.v342.zip

The version v342 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

Please note description of new features in this release and history of features:

http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features#13_Dec_2016.2C_v342

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:
http://genome.ucsc.edu/license/

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

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

October 2016 note: v339 changed name of phyloGif to phyloPng

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

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

Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene

hgGenome hgGtexTrackSettings hgHubConnect hgIntegrator hgLiftOver hgLogin

[Hiram Clawson]

Good Evening Genome Browser Mirror Site Operators:

The version v344 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.v344.zip

The version v344 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

Please note description of new features in this release and history of features:

http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features#7_Feb_2017.2C_v344

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v345 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.v345.zip

The version v345 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

Please note description of new features in this release and history of features:

http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features#28_Feb_2017.2C_v345

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:
http://genome.ucsc.edu/license/

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

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

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v346 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.v346.zip

The version v346 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v347 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.v347.zip

The version v347 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:
http://genome.ucsc.edu/license/

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

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

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

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/v347.html

http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v348 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.v348.zip

The version v348 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):
***** 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

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

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/v348.html

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v349 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.v349.zip

The version v349 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

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

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/v349.html

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v350 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.v350.zip

The version v350 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

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

June 2017 note: v350 has a new CGI binary: hgGeneGraph with associated files
in cgi-bin/pyLib/ and cgi-bin/loader/dot_static

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/v350.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

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/*

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v351 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.v351.zip

The version v351 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/v350.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

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v352 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.v352.zip

The version v352 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v357 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.v357.zip

The version v357 CGI binaries can be found at:

http://genecats.soe.ucsc.edu/builds/versions-all/v357.html

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v358 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.v357.zip

The version v358 CGI binaries can be found at:

http://genecats.soe.ucsc.edu/builds/versions-all/v358.html

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v359 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.v359.zip

The version v359 CGI binaries can be found at:

http://genecats.soe.ucsc.edu/builds/versions-all/v359.html

[Hiram Clawson]

Good Evening Genome Browser Mirror Site Operators:

The version v360 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.v360.zip

The version v360 CGI binaries can be found at: