v329 Genome Browser Available

[Brian Raney]

Good Morning Genome Browser Mirror Site Operators:

The version v329 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.v329.zip
<http://hgdownload.soe.ucsc.edu/admin/jksrc.v329.zip>

The version v329 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.

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March 9 note: 

NEW multi-region display slices tracks by exons, genes, haplotype or coordinates! Read more at the announcement:http://bit.ly/1R4STNM Or on the Multi-Region User Guide: http://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html

Here's an example Exon-Only Session: http://bit.ly/1nv1K3M Use the shortcut "d v" to return to the "default view" and "e v" to enter "exon view" (and "?" to see all shortcuts). Or click the top blue "View" menu and then "Multi-Region", or the new "multi-region" button below the browser window to see more options.

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*****
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/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)

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, 
Brian