v324 Genome Browser Available

[Galt Barber]

Good Afternoon Genome Browser Mirror Site Operators:

The version v324 source is now available at:
       http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:
       http://hgdownload.soe.ucsc.edu/admin/jksrc.v324.zip

The version v324 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/

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.

*****
NOTE: The genome browser system can now be obtained 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 hgRenderTracks hgSession hgSuggest hgTables hgTrackUi hgTracks
hgUserSuggestion hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloGif

(note: new binaries with:
    release v317: hgIntegrator June 2015,
    release v318: hgMenubar June 2015)

  and these configuration files:

/usr/local/apache/cgi-bin/all.

joiner
/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/*

(note: new configuration file: release v323: extTools.ra October 2015)

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 now available at:
   http://hgdownload.cse.ucsc.edu/admin/

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

Thanks, Galt

[Galt Barber]

We just updated our release v324 to fix a couple of minor problems.

One was for an incorrect dropdown menu label in hgTracks,
another was for links with #anchor in the URL such as appear in some hgc/hgGene gene details pages.

-Galt

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v325 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v325.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v325.zip>

The version v325 CGI binaries can be found at:

Thanks, Hiram

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v326 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v326.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v326.zip>

The version v326 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/

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.

*********************************************************************
December 2015 note: v326 release added a new hg.conf option:

suppressVeryEarlyErrors=on

This will show 500 errors instead of "very early" error messages.
*********************************************************************

*****
NOTE: The genome browser system can now be obtained 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 hgGeneog

hgGenome hgHubConnect hgIntegrator hgLiftOver hgLogin hgMenubar hgMirror
hgNear hgPal hgPcr hgRenderTracks hgSession hgSuggest hgTables hgTrackUi
hgTracks hgUserSuggestion hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloGif

(note: new binaries with:
release v317: hgIntegrator June 2015,
release v318: hgMenubar June 2015)

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/*

(note: new configuration file: release v323: extTools.ra October 2015,
updated encode/cv.ra file release v326 December 2015)

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v327 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v327.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v327.zip>

The version v327 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/

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.

*********************************************************************
December 2015 note: v326 release added a new hg.conf option:

suppressVeryEarlyErrors=on

This will show 500 errors instead of "very early" error messages.
*********************************************************************

*****
NOTE: The genome browser system can now be obtained 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

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v328 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v328.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v328.zip>

The version v328 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v331 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v331.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v331.zip>

The version v331 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v332 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v332.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v332.zip>

The version v332 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/

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.

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

May 2016 note: v332 release added a new hg.conf option:

# Display phylogenetic tree in hgGateway (URL relative to cgi-bin)
hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js

This turns on the display of a phylogenetic tree and selection diagram
on the gateway page.

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v333 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v333.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v333.zip>

The version v333 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v334 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v334.zip

The version v334 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#21_June_2016.2C_v334

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.

*********************************************************************
May 2016 note: v332 release added a new hg.conf option:

# Display phylogenetic tree in hgGateway (URL relative to cgi-bin)
hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js

This turns on the display of a phylogenetic tree and selection diagram
on the gateway page.

***************************
December 2015 note: v326 release added a new hg.conf option:

suppressVeryEarlyErrors=on

This will show 500 errors instead of "very early" error messages.
*********************************************************************

*****

NOTE: The genome browser system can 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 phyloGif

(note: new binaries with:

release v334: hgPublicSessions June 2016,

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v335 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v335.zip

The version v335 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#12_July_2016.2C_v335

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/

*********************************************************************
May 2016 note: v333 release added new hg.conf options:

# allow automatic density graph display for feature-based tracks when
# too many items to display
canDoCoverage=on

# enable CRAM data types display
cramRef=/userdata/cramCache
# see also: src/product/README.cram
# and: http://www.ebi.ac.uk/ena/software/cram-toolkit

***************************
May 2016 note: v332 release added a new hg.conf option:

# this setting is on by default, not required in hg.conf

# Display phylogenetic tree in hgGateway (URL relative to cgi-bin)
hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js

# to disable the display of the phylogenetic tree, enter an empty statement:
hgGateway.dbDbTaxonomy=

***************************
December 2015 note: v326 release added a new hg.conf option:

suppressVeryEarlyErrors=on

This will show 500 errors instead of "very early" error messages.
*********************************************************************

*****

NOTE: The genome browser system can be used in a Virtual Box VM

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

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v336 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v336.zip

The version v336 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#2_August_2016.2C_v336

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/

*********************************************************************
May 2016 note: v333 release added new hg.conf options:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v337 source is now available at:

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v337.zip

The version v337 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#23_August_2016.2C_v337

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v338 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.v338.zip

The version v338 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_September_2016.2C_v338