Cluster::Jobs - A Perl module for submitting scripts to a job manager/scheduler
Description
Cluster::Jobs provides a Perl interface to submit sequential and parallel jobs to a job manager/scheduler like HTCondor or TORQUE. Jobs can also be executed locally with bash or make.
Synopsis
use FindBin qw($Bin);
use lib "$Bin/lib/Cluster";
use Jobs;
my $job = Jobs->new( -config => "config.ini");
## e.g.
## 2 bwa scripts created beforehand
$job->add_job(script => "test.sh" , name => "test" , program => "bwa");
$job->add_job(script => "test2.sh", name => "test2", program => "bwa", dependency => "test");
## test2.sh will run after test.sh
$job->submit("test_bwa");
Config file format (Config::IniFiles)
[job]
manager=bash # condor|make|torque
[bwa]
cmd=/NGS/ngs_pipeline/bin/bwa-0.7.12/bwa
cpu=4 # number of cpu/core needed for condor/torque.
mem=9 # Maximum amount of memory for condor/torque (4 = 4GB).
time=82:01:02 # Maximum running time for torque (HH:MM:SS).
[make]
cpu=2 # make will run 2 jobs in parallel when used as a job manager.
Requirements
Cluster::Jobs use the perl modules Config::IniFiles and IPC::Cmd
## install from cpan
cpan -i Config::IniFiles IPC::Cmd
Alternatives
- Grid::Request - An API for submitting jobs to a computational grid such as SGE or Condor.
- HPCI - High Performance Computing Interface
- PBS::Client - Perl interface to submit jobs to Portable Batch System (PBS).