[genome-mirror] v437 Genome Browser Available
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Christopher Lee
Oct 5, 2022, 12:53:49 PM10/5/22
to genome-mirror
Good Morning Genome Browser Mirror Site Operators:
The version v437 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.v437.zip
The version v437 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
*********************************************************************
August 2018 note: v369 was the last build to take place in our CentOS 6.8
environment; builds are now on CentOS 7.5. Copies of v369 binaries will be
maintained for a while at
ftp://hgdownload.soe.ucsc.edu/apache/cgi-bin.v369/ and
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/.
*********************************************************************
Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions-all/v437.html
The following CGIs were updated:
cartDump cartReset das hgApi hgBlat hgCollection 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 hubApi
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.
ChrisL
UCSC Genomics Institute
The version v437 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.v437.zip
The version v437 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
*********************************************************************
August 2018 note: v369 was the last build to take place in our CentOS 6.8
environment; builds are now on CentOS 7.5. Copies of v369 binaries will be
maintained for a while at
ftp://hgdownload.soe.ucsc.edu/apache/cgi-bin.v369/ and
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/.
*********************************************************************
Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions-all/v437.html
The following CGIs were updated:
cartDump cartReset das hgApi hgBlat hgCollection 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 hubApi
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.
ChrisL
UCSC Genomics Institute
![McCully, Dwayne (NIH/NIAMS) [C]'s profile photo](https://lh3.googleusercontent.com/a/default-user=s40-c)
McCully, Dwayne (NIH/NIAMS) [C]
Oct 5, 2022, 3:44:19 PM10/5/22
to Christopher Lee, genome...@soe.ucsc.edu
Hi Christopher,
I use the browserSetup.sh to keep my mirror up to date but should I run the hgcentral.sql script against my mariadb database each time I see this e-mail. See below.
Dwayne
-----Original Message-----
From: 'Christopher Lee' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu>
Sent: Wednesday, October 5, 2022 12:54 PM
To: genome-mirror <genome...@soe.ucsc.edu>
Subject: [EXTERNAL] [genome-mirror] v437 Genome Browser Available
Good Morning Genome Browser Mirror Site Operators:
The version v437 source is now available at:
https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fadmin%2Fjksrc.zip&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Mvx2Jne32UHvZwEXbfqGY35HFNujJge4LQYAy5n2icI%3D&reserved=0
or labeled with version number:
https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fadmin%2Fjksrc.v437.zip&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OVo8bZjDx6toIT%2FY2S0wEZbqKw8xYIZHFAEZoty07jc%3D&reserved=0
The version v437 CGI binaries can be found at:
rsync -avP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: https://gcc02.safelinks.protection.outlook.com/?url=ftp%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fapache%2Fcgi-bin%2F&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ILAqM46lnSon0jhjkwy0S7%2FPGO%2FGNggszvcogHbvxV4%3D&reserved=0
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://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome.ucsc.edu%2Flicense%2F&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wrIFhNUFdUT%2BwhSNIRw2fVb%2FE4pd8Alqx6GnAkIsbhc%3D&reserved=0
See also: https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgenome.ucsc.edu%2FgoldenPath%2Fhelp%2Fmirror.html&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0nh9%2B1yfQ9XKHnQ2hH6ooRmXSg45FUw09zASLkZ5Gto%3D&reserved=0
*********************************************************************
***** 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://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome-store.ucsc.edu%2F&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=z9u0mrzemzi2gLoUMmO6isTjDXYaTfYe7vtM4E%2B%2BicA%3D&reserved=0
***** See also: https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome.ucsc.edu%2Fgoldenpath%2Fhelp%2Fgbic.html&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=O%2BRI2g7uLSK6l5fquwOheRGvcqqHEMAnf1ya9l%2Bic3A%3D&reserved=0
***** The genome browser system can be used in a Virtual Box VM
NOTE: image from the 'Genome Store': https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome-store.ucsc.edu%2F&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=z9u0mrzemzi2gLoUMmO6isTjDXYaTfYe7vtM4E%2B%2BicA%3D&reserved=0
***** See also: https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome.ucsc.edu%2FgoldenPath%2Fhelp%2Fgbib.html&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G5C78WnEpk8q2D%2BbfboeSS%2FOfsuLrWHAgzxALw%2FccqU%3D&reserved=0
*********************************************************************
August 2018 note: v369 was the last build to take place in our CentOS 6.8 environment; builds are now on CentOS 7.5. Copies of v369 binaries will be maintained for a while at
https://gcc02.safelinks.protection.outlook.com/?url=ftp%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fapache%2Fcgi-bin.v369%2F&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=96%2BWr1o%2BqeTyLb5qQt3iTSELO3MZq8l8%2ByOW0hIX7IQ%3D&reserved=0 and https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fadmin%2Fexe%2Flinux.x86_64.v369%2F&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ANDqZjIp2EjGNUjT2Zv7L%2B9AvXwCzyE%2BT4AYHAyFAW0%3D&reserved=0.
*********************************************************************
Summaries of changes for this version update can be found here:
https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgenecats.soe.ucsc.edu%2Fbuilds%2Fversions-all%2Fv437.html&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9e8Az6Kiuvxxeteklb74iWNkQ9ir3ixUzI%2Bt9%2BOM%2FNg%3D&reserved=0
The following CGIs were updated:
cartDump cartReset das hgApi hgBlat hgCollection 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 hubApi 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:
https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fhgdownload.soe.ucsc.edu%2Fadmin%2Fhgcentral.sql&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gdrIckdKIZhgrdOvOdg5SeakjTiSc1U%2B8DN8qCIURXI%3D&reserved=0
If you have any questions or concerns, please feel free to write back to this genome-mirror mail list.
ChrisL
UCSC Genomics Institute
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CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
I use the browserSetup.sh to keep my mirror up to date but should I run the hgcentral.sql script against my mariadb database each time I see this e-mail. See below.
Dwayne
-----Original Message-----
From: 'Christopher Lee' via UCSC Genome Browser Mirror-Specific Support <genome...@soe.ucsc.edu>
Sent: Wednesday, October 5, 2022 12:54 PM
To: genome-mirror <genome...@soe.ucsc.edu>
Subject: [EXTERNAL] [genome-mirror] v437 Genome Browser Available
Good Morning Genome Browser Mirror Site Operators:
The version v437 source is now available at:
or labeled with version number:
The version v437 CGI binaries can be found at:
rsync -avP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ${WEBROOT}/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:
See also: https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgenome.ucsc.edu%2FgoldenPath%2Fhelp%2Fmirror.html&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0nh9%2B1yfQ9XKHnQ2hH6ooRmXSg45FUw09zASLkZ5Gto%3D&reserved=0
*********************************************************************
***** The genome browser system can be installed on a linux system
NOTE: with the 'GBiC' script (Genome Browser in the Cloud) from
***** See also: https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome.ucsc.edu%2Fgoldenpath%2Fhelp%2Fgbic.html&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=O%2BRI2g7uLSK6l5fquwOheRGvcqqHEMAnf1ya9l%2Bic3A%3D&reserved=0
***** The genome browser system can be used in a Virtual Box VM
***** See also: https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome.ucsc.edu%2FgoldenPath%2Fhelp%2Fgbib.html&data=05%7C01%7Cdmccully%40mail.nih.gov%7C8e008c0cd24649a8222408daa6f23061%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638005857300932035%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G5C78WnEpk8q2D%2BbfboeSS%2FOfsuLrWHAgzxALw%2FccqU%3D&reserved=0
*********************************************************************
August 2018 note: v369 was the last build to take place in our CentOS 6.8 environment; builds are now on CentOS 7.5. Copies of v369 binaries will be maintained for a while at
*********************************************************************
Summaries of changes for this version update can be found here:
The following CGIs were updated:
cartDump cartReset das hgApi hgBlat hgCollection 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 hubApi 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:
If you have any questions or concerns, please feel free to write back to this genome-mirror mail list.
ChrisL
UCSC Genomics Institute
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Maximilian Haeussler
Oct 6, 2022, 12:18:03 PM10/6/22
to McCully, Dwayne (NIH/NIAMS) [C], Christopher Lee, genome...@soe.ucsc.edu
Hi Dwayne,
the answer to your question depends on whether you have non-UCSC assemblies on your mirror or public hubs and whether these have special blat servers that you host at NIH. If yes, applying our hgcentral.sql file will delete all those, the genomes and their blat server links.
However, we move around our blat servers every few years. So you will have to load hgcentral.sql at some point from us. This is why the browserSetup.sh script does it on every cgi-update.
Right now, the browserSetup.sh has no logic to merge your special local tables and blat servers with hgcentral.sql. If you need that, we could add that to the script... Ideally, you would add your local assemblies, blat servers and public hubs to special tables, then run the script and the script will merge your tables with the tables from hgcentral.sql. That only requires that your local entries do not overlap with ours, so you just add to the assemblies, you don't modify them. Would that work?
best
Max
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