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Revision 1.1 - (download) (as text) (annotate)
Fri Mar 23 20:41:31 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, mgrast_rel_2008_0806, mgrast_dev_10262011, mgrast_dev_02212011, mgrast_rel_2008_0923, mgrast_release_3_0, mgrast_dev_03252011, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, mgrast_rel_2008_0919, mgrast_rel_2008_1110, myrast_33, mgrast_rel_2008_0917, mgrast_dev_04052011, mgrast_dev_02222011, HEAD
initial checking of metagenome 48 stuff

#
# Trivial script that is submitted as a postprocessor to the sims runs that marks
# the sims stage as complete.
#

use strict;
use FIG;
use FIG_Config;
use File::Basename;
use GenomeMeta;
use Job48;
use SGE;

my $STAGE = "sims";

@ARGV == 1 or die "Usage: $0 job-dir\n";

my $jobdir = shift;

-d $jobdir or die "$0: job dir $jobdir does not exist\n";

my $job_id = basename($jobdir);
my $job = new Job48($job_id);

my $meta = $job->meta;

print "Running job! $jobdir\n";

$job->meta->set_metadata("status.$STAGE", "complete");
$job->meta->set_metadata("$STAGE.running", "no");

sub run
{
    my(@cmd) = @_;
    
    print "Run @cmd\n";
    my $rc = system(@cmd);
    if ($rc != 0)
    {
	&fatal("Failed with rc=$rc: @cmd");
    }
}

sub fatal
{
    my($msg) = @_;

    $meta->add_log_entry($0, ['fatal error', $msg]);
    $meta->set_metadata("status.$STAGE", "error");

    croak "$0: $msg";
}
    

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