Script Example

The scripts for analysis operations are generated from templates (​Template Example). Every script for execution on a cluster consists of a header and body. Besides other parameters, a cluster header contains information about the maximum operation execution time. Execution will be stopped, if it exceeds the maximum time. Operations shorter than 30 minutes are submitted to the short Millipede cluster queue:

# execution time = 5 hours
#PBS -l walltime=05:00:00 

Additionally, a header contains path to the files, where command-line output and error will be written:

#PBS -e /data/user123/monitor/analysis1/job1_step02.err
#PBS -o /data/user123/monitor/analysis1/job1_step02.out

A script body contains supplementary print-out commands used for ​logging/monitoring of job execution and a main command line, which is an invokation of an analysis tool.

# convert to ped+map format
# log start-time
printf "gwa1foranalysis_step0_started convert to ped+map format" >>/data/user1/job1/monitor.txt
date "+DATE: %m/%d/%y%tTIME: %H:%M:%S" >>/data/user1/job1/monitor.txt
# analysis
/data/user1/exes/plink --noweb --bfile /data/user1/data/job1/gwa1foranalysis --recode --out /data/user1/data/job1/ped/gwa1foranalysis
#log finish-time
printf "gwa1foranalysis_step0_finished " >>/data/user1/job1/monitor.txt
date "+DATE: %m/%d/%y%tTIME: %H:%M:%S" >>/data/user1/job1/monitor.txt

In this way, we have several level of logging information:

• about job start and finish time, which is used in workflow management (printing in a script body)
• about job results, which is used in error-handling (printing in a script header)

Back to ​Examples