Cronjobs
Contents
Restart the blat server
Root privileges: yes
Runs on: all nodes
0 4 * * * /usr/local/wormbase/util/admin/restart_blat.pl
Checks whether the blat servers (gfServer) for C. elegans and C. briggsae are running and restarts them if not. It retrieves configuration information directly from elegans.pm and determines versions of the databases (when restarting) from the status information stored in acedb.
Update the production nodes
Root privileges: no
Runs on: all production nodes
1 1 * * * /usr/local/bin/wb_update_wormbase.pl > /usr/local/wormbase/logs/update.log
Checks for a new release of the database. If present, installs it. If not, simply updates the software.
Keep the production module up-to-date
Root privileges: no
Runs on: brie3
15 * * * * /usr/local/wormbase-admin/update_scripts/maintain_production_module.pl
Copy select files into the staging directory at /usr/local/wormbase-production so that they can be copied over to the production nodes.
Keep the citations list up-to-date
Root privileges: no
Runs on: brie3
0 0 1 * * /usr/local/wormbase-admin/update_scripts/fetch_literature_citations.sh
Once a month, fetch the updated Endnote formatted literature list from Hans-Michael at Caltech.
Maintain support files for standard URLs
Root privileges: no
Runs on: brie6
0 2 * * * /usr/local/wormbase-admin/update_scripts/maintain_standard_urls.pl
Serves to copy over files from the FTP site hosted on brie3 so that they can be served by the standard URLs system in place. Alternatives:
- The standard URLs code should be modified to support remote hosts
- Standard URLs should be handled entirely by squid
Update the Google Site Map
Root privileges: no
Runs on: brie6
Generate new sitemap thrice weekly (total overkill) #0 4 * * 0,2,4 /usr/local/wormbase/util/google_indexing/create_sitemap.sh 0 4 * * 0,3 /usr/local/wormbase-admin/google_indexing/create_sitemap.sh
Clean up GBrowse debris
cd $HTDOCS/gbrowse/tmp # replace with correct tmp directory find . -type f -atime +20 -print -exec rm {} \; # remove old files & uploads find . -type d -empty -depth -print -exec rmdir {} \; # remove empty directories
Maintain our CPAN archive
$ cpan -u tharris -e * 3 * * * minicpan