Cronjobs

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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:

  1. The standard URLs code should be modified to support remote hosts
  2. 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

Root privileges: no Runs on: wb-dev

$ cpan -u tharris -e
* 3 * * * minicpan