Deploying scripts at specific times

Some operations must be executed from time to time, for instance, checking if mail has arrived or making a back up. Usually these tasks are done by the system itself, but an user may also want to register some of his/her scripts to be automatically executed at some times.

Calling the scripts is done by the process cron, which is started at boot time -- you do not need to run the program yourself. If you want to schedule a task, all you have to do is to register it in the system, using an auxiliary tool called crontab.

This tool updates the cron table (hence the name) of tasks. To register a task you need to say what should be executed and how often it should run. This is done by writing a line with six fields, in this order: minute, hour, day of month, month, day of week and the command. The fields are separated by spaces or tabs.

As you can see, the first five fields specify the time and seem to very restrictive, but in fact each of them can be very flexible. An * means any value and ranges or lists are allowed. This is best explanied by some examples (you may want to try them):

• * * * * * date >> ~/Timespamps
  This will update the file ``Timesptamps'' in the user's home directory every minute.
• */5 * * * * date >> ~/Timespamps
  Will do the same, but every 5 minutes.
• 30 7-10,17-20 * * 1-5 date >> ~/Timespamps
  The update will occur on weekdays, at these times: 7:30h, 8:30h, 9:30h, 10:30h, 17:30h, 18:30h, 19:30h and 20:30h.
• The following line will send an email to curie@somewhere.fr every November, $7^{\mbox{\scriptsize th}}$ with a birthday message.

  0  8  7 11 * echo "Happy birthday, Marya!" | mail -s "For you" curie@somewhere.fr
  

In the command, any % is transformed into newline, and anything after the first % is passed to the standard input of the command. The last example above could be written as:

0  8  7 11 *  mail "For you" curie@somewhere.fr % Happy Birthay, Marya! %% myself %

You need to write the list of tasks in a file and call crontab to register them. You can check the current list you have by issuing

crontab -l

If you prefer, you can edit the system copy of your list directly with crontab -e. To remove all your tasks from the system, use crontab -r.

• what is batch processing? (GUBI)
• Shell scripts In bioinformatics, there are many tasks that have to be repeated constantly. One example is updating local versions of sequence databases. These tasks in general involve running more than one program. Following on our example, one may need to, after downloading the updated version of sequences databases, to run BLAST on sequences that were generated locally, to check if there is any new match. In Linux there is a very easy way to created little ``programs'', the shellscripts that perform many shell commands. It is similar to the old ``.bat'' files of Windows. To create a shellscript you only need to create a file where, in each line, you type the Linux command to be executed. After you finished editing the file, save it, and add ``excecution'' permission to it. Now you file can be run as any normal Linux program. When you run this file, all Linux commands will be performed in the order you specified.

• cron (GUBI)