Updating a Genome Browser Mirror: Difference between revisions

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(New page: To update your local Genome Browser Installation: * As root, cd to your cgi-bin directory and update the cgi-bin files: cd /var/www/cgi-bin rsync -avzP rsync://hgdownload.cse.ucsc.edu...)
 
(changed cse to soe)
 
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To update your local Genome Browser Installation:
* As root cd to your html directory and update all html/javascript/image files:
 
  cd /var/www/html
* As root, cd to your cgi-bin directory and update the cgi-bin files:
  rsync -avzP rsync://hgdownload.soe.ucsc.edu/html/ ./
* As root, cd to your cgi-bin directory and update the cgi-bin files (=the programs of the browser):
   cd /var/www/cgi-bin
   cd /var/www/cgi-bin
   rsync -avzP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ./
   rsync -avzP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ./
* go to your mysql directory and update the mysql tables. For each assembly, cd into its directory and run rsync like this:
* go to your mysql directory and update the mysql tables. For each assembly, cd into its directory and run rsync like this:
   cd /var/lib/mysql/mm9
   cd /var/lib/mysql/mm9
   rsync -avzP rsync://hgdownload.cse.ucsc.edu/mysql/mm9/ ./
   rsync -avzP rsync://hgdownload.soe.ucsc.edu/mysql/mm9/ ./
As you might have modified your mirror, do not use the "--delete" option in this rsync command, as it would just overwrite your modifications.
As you might have modified your mirror, do not use the "--delete" option in this rsync command, as it would just overwrite your modifications.
* Update the Genbank files:
* Update the Genbank files, most assemblies link to them in some way and they don't work without these files:
   cd /gbdb/genbank
   cd /gbdb/genbank
   rsync -avzp rsync://hgdownload.cse.ucsc.edu/gbdb/genbank/ ./
   rsync -avzp rsync://hgdownload.soe.ucsc.edu/gbdb/genbank/ ./

Latest revision as of 07:54, 1 September 2018

  • As root cd to your html directory and update all html/javascript/image files:
 cd /var/www/html
 rsync -avzP rsync://hgdownload.soe.ucsc.edu/html/ ./
  • As root, cd to your cgi-bin directory and update the cgi-bin files (=the programs of the browser):
 cd /var/www/cgi-bin
 rsync -avzP rsync://hgdownload.soe.ucsc.edu/cgi-bin/ ./
  • go to your mysql directory and update the mysql tables. For each assembly, cd into its directory and run rsync like this:
 cd /var/lib/mysql/mm9
 rsync -avzP rsync://hgdownload.soe.ucsc.edu/mysql/mm9/ ./

As you might have modified your mirror, do not use the "--delete" option in this rsync command, as it would just overwrite your modifications.

  • Update the Genbank files, most assemblies link to them in some way and they don't work without these files:
 cd /gbdb/genbank
 rsync -avzp rsync://hgdownload.soe.ucsc.edu/gbdb/genbank/ ./