Gbib auto updates

Jorge's Sunday update of hgdownload is run by /root/mirror-mysql-apache-gbdb. At the end, it runs the command "touch /mirrordata/gbib/lastUpdate".

By default the Gbib update script /root/updateBrowser.sh checks every few minutes if the flag file on the hgDownload server http://hgdownload.soe.ucsc.edu/gbib/lastUpdate is more recent than the date of the last update of the Gbib. This check is randomly spread over 30 seconds (crontab + /root/cronUpdate.sh).

Auto updates can be deactivated on a box with autoUpdateOff and reactivated with autoUpdateOn.

By supplying the parameter "notSelf" to updateBrowser, the box will skip this check and update without checking the flag file.

If the file on hgDownload is newer than the flagfile, it will start the update (/root/updateBrowser.sh):

1. Update the update script itself from hgdownload.soe.ucsc.edu/gbib
2. Update all existing /gbdb files
3. Update all mysql files
4. Update all hgcentral files + patch the blat server table
5. Patch the menu to remove hgNear and add hgMirror
6. Place the symlink to /media from htdocs/folders
7. Run hgMirror to hide some tracks on hg19 and remove some searches from hg19

updateBrowser.sh also accepts an option: "hgwdev <hgwdevUsername> <cgiSuffix>". These pull the CGIs from hgwdev into the current gbib. "updateBrowser hgwdev" shows some more help and examples.

Note that if you have downloaded other binaries than the release ones, then the box will loose them by auto-updating to release state again on the next Sunday, when hgdownload is updated. If you do not want to have your special CGIs/htdocs overwritten, deactivate auto updates on your own gbib. Auto updates can be deactivated on a box with autoUpdateOff and reactivated with autoUpdateOn. You can also run VBoxManage guestproperty set browserbox gbibAutoUpdateOff yes more here.

See this lastUpdate file note about how if you have a beta candidate, after the beta week, the Sunday touch of hgdownload files will update the date of lastUpdate and trigger your beta to update to the version on hgdownload.

Here is also a picture of the MySQL data flow.

The flow of other GBiB data (/gbdb /cgi-bin /htdocs) is similar, where the data ends up on hgdownload. The following rsync command reflects how the data exists at hgdownload:

 rsync rsync://hgdownload.soe.ucsc.edu

genome         	UCSC Human Genome Downloads
sars           	UCSC Human Genome SARS Downloads
htdocs         	UCSC Human Genome Web Site Htdocs
goldenPath     	UCSC Human Golden Path Downloads
cgi-bin        	UCSC Human Genome Web Site CGI Binaries x86_64
cgi-bin-i386   	UCSC Human Genome Web Site CGI Binaries i386
gbdb           	UCSC Human Genome Browser Gbdb Config Files
archives       	UCSC Human Genome Browser Archived Config Files
mysql          	UCSC Human Genome Raw Mysql Tables
gbib           	UCSC Genome Browser in a Box
hubs           	UCSC Genome Browser Public Hubs