Updating a Genome Browser Mirror: Difference between revisions
From genomewiki
Jump to navigationJump to search
(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) |
||
| (One intermediate revision by one other user not shown) | |||
| Line 1: | Line 1: | ||
* 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. | 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. | 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. | 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/ ./
