Gbib auto updates

By default the Gbib update script /root/updateBrowser.sh checks every minute if a flag file on the hgDownload server 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).

By supplying the parameter "force" 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 hgwdev.soe.ucsc.edu/browserbox and also update the hg.conf from there
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: either "alpha", "beta" or "devbox". These pull the CGIs from hgwdev. They don't use rsync but a normal http download which has to be prepared first with "boxPrep alpha|beta|devbox" as qateam on hgwdev.

Note that if you have updated to alpha/beta/devbox state once, then the box won't update anymore from hgdownload until the next Sunday, when hgdownload is recreated.

Note: Will have to move updateBrowser.sh and hg.conf to hgdownload for release.

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