1. Unix Scripts and PBS on BioU
Alexander J. Ropelewski

2. Unix Scripts
Type
Run
Save File

3. A Very Simple Script #!/bin/sh # # run the ls command ls -laF
File: mylsscript.sh

4. A Very Simple Script #!/bin/sh # # run the ls command ls -laF
FIRST LINE: Tells the UNIX System the Shell (or command interpreter) to use. Can be:
#!/bin/sh
#!/bin/csh
#!/bin/tcsh
#!/usr/bin/perl
Or many others…
#!/bin/sh #
# run the ls command
ls -laF
Lines beginning with # are comments
File: mylsscript.sh
The UNIX command(s) to execute, in this case we want the ls command

5. Steps to Running a Script
Edit a file
Place commands in file
Save File
Make File Executable:
chmod u+x mylsscript.sh
Type in the name of the script file
mylsscript.sh

6. What can Scripts Do Scripts can assign values to variables
Scripts can have control elements such as:
Error Checking
Conditionals (If Tests)
Loops
Scripts can also do simple math
Scripts can run programs

7. Script With Conditional & Error Check
#!/bin/sh
cp file.out $HOME/file.out
if [ $? -eq 0 ]
then
echo "File copied"
else
echo "PROBLEM" fi
File: iftest.sh

8. Script With Conditional & Error Check
Test condition: $? Is the status returned from the prior command (cp). If the prior command (cp) was successful, this will contain 0
First line tells us this is a Bourne Shell Script
Copy command
#!/bin/sh
cp file.out $HOME/file.out
if [ $? -eq 0 ]
then
echo "File copied"
else
echo "PROBLEM" fi
Conditional test; format must be either :
IF - THEN - FI
-or-
IF - THEN - ELSE - FI
If condition is true write “File copied” message
If condition is false write “PROBLEM” message
File: iftest.sh

9. Script With Loop & Simple Math
#!/bin/sh
i="1"
while [ $i -le 180 ] do
echo "Iteration # $i"
i=`expr $i + 1`
sleep 1
done
File: test1.job

10. Script With Loop & Simple Math
First line tells us this is a Bourne Shell Script
Condition: variable i is less than or equal to 180
Initialize variable i to 1
#!/bin/sh
i="1"
while [ $i -le 180 ] do
echo "Iteration # $i"
i=`expr $i + 1`
sleep 1
done
While Loop: Do the instructions between the do and done until the condition is satisfied
Echo command is a simple print function.
Assign variable i to now be equal to the old value of i plus 1.
Sleep command tells system to wait 1 second before continuing
File: test1.job

11. What Are PBS Scripts
PBS scripts are just Unix shell scripts with some additional attributes (that provide resource and control information) that are executed by the PBS queuing system.
PBS scripts are submitted to queues and are run when the system has resources available
PBS script files will be created and run for you automatically when you use the Galaxy interface on BioU
You can gain more control over your analyses by writing (and running) your own PBS scripts
Sometimes you will hear PBS scripts called "jobs".

12. PBS Script With Loop & Simple Math
#!/bin/sh
#PBS -q serial
#PBS -j oe
#PBS -l walltime=00:10:00
#PBS -l nodes=1:ppn=1
#PBS -N PbsTest
i="1"
while [ $i -le 180 ] do
echo "Iteration # $i"
i=`expr $i + 1`
sleep 1
done
File:
pbstest.job

13. PBS Script With Loop & Simple Math
Parameters always begin with: #PBS
Queue name: On BioU these are serial and parallel
Write stderr in stdout file
#!/bin/sh
#PBS -q serial
#PBS -j oe
#PBS -l walltime=00:10:00
#PBS -l nodes=1:ppn=1
#PBS -N PbsTest
i="1"
while [ $i -le 180 ] do
echo "Iteration # $i"
i=`expr $i + 1`
sleep 1
done
Set the walltime limit to ten minutes
Serial job, so only need one core on one node.
Name the job PbsTest
File: pbstest.job

14. Running PBS Scripts
To submit a PBS script use the qsub command: % qsub pbstest.job 382.biou1.psc.edu The system will respond with the PBS identifier: 382 – The scripts job id number biou1.psc.edu - The computer id

15. Monitoring PBS Scripts
To see if a PBS script is running, use the qstat command:
% qstat
Job id Name User Time Use S Queue
381.biou serial_example nigra R serial
382.biou pbstest.job ropelews Q serial

16. Killing PBS Scripts
To kill a PBS script, first, get the PBS script identifier:
% qstat
Job id Name User Time Use S Queue
381.biou serial_example nigra R serial
382.biou pbstest.job ropelews Q serial
Then terminate the PBS script:
% qdel 382.biou1

17. Galaxy PBS Scripts
To check on a PBS script submitted through Galaxy, use the BioU status check tool.
Galaxy PBS scripts are limited to 48 hours (walltime)
PBS scripts submitted through Galaxy can not be terminated by the user.
PBS scripts submitted on the command line can run longer than 48 hours.