NAME
Bio::Grid::Run::SGE::Job - the container for settings and important functions
SYNOPSIS
use Bio::Grid::Run::SGE::Job;
my $j = Bio::Grid::Run::SGE::Job->new;
$j->run(
pre_task => sub {...},
task => sub {...},
post_task => sub {...},
usage => sub {...}
);
DESCRIPTION
This class is never created directly, it is always created via L <Bio::Grid::Run::SGE> and exported as C <job()> function:
use Bio::Grid::Run::SGE;
my $j = job();
$j->run(...);
ATTRIBUTES
my $log = $j->log()
Returns a Bio::Gonzales::Util::Log logging instance. Useful functions are
$log-
debug("text")>$log-
info("text")>$log-
warn("text")>$log-
error("text")>$log-
fatal("text")>$log-
fatal_confess("text")>
METHODS
Settings-related
- my $job_config = $j->conf or my $job_config = $j->config
-
Get (or change) the job configuration.
- my $job_environment = $j->env
-
Get the job environment.
You can also change stuff, but be careful; you have been warned!
- my $job_id = $j->job_id
-
The same as
$j-
env('job_id')>. - my $task_id = $j->task_id
-
The same as
$j-
env('task_id')>.
System call-related
- $j->sys(@command)
-
Runs command eiter as array or as simple string (see also system) and gives a warning message if something goes wrong.
It returns
undef
is something went wrong and 1 if the exit code of the program was ok. - $j->sys_fatal(@command)
-
Runs command eiter as array or as simple string (see also system) and dies if something goes wrong.
- $j->sys_pipe(@command)
- $j->sys_pipe_fatal(@command)
LIMITATIONS
SEE ALSO
AUTHOR
jw bargsten, <jwb at cpan dot org>