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Revision 1.1 - (download) (as text) (annotate)
Fri May 2 16:55:44 2008 UTC (11 years, 7 months ago) by mkubal
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, 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, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
for new RAST genomes

#
# Run PSORT and create attributes data.
#

use Data::Dumper;
use Carp;
use strict;
use FIG;
use FIG_Config;
use File::Basename;
use GenomeMeta;
use Sim;

@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 $hostname = `hostname`;
chomp $hostname;

my $genome = &FIG::file_head("$jobdir/GENOME_ID");
chomp $genome;
$genome =~ /^\d+\.\d+/ or die "$0: Cannnot find genome ID for jobdir $jobdir\n";

my $meta = new GenomeMeta($genome, "$jobdir/meta.xml");

my $genome_dir = "$jobdir/rp/$genome";

my @apps = qw(rp_run_PSORT_on_genome
	      rp_make_PSORT_attributes
	      rp_index_attributes
	     );

$meta->set_metadata("psort.hostname", $hostname);

for my $app (@apps)
{
    $meta->add_log_entry($0, "start $app on $hostname in $jobdir");
    
    my $cmd = "$FIG_Config::bin/$app $jobdir $genome > $jobdir/rp.errors/$app.stderr 2>&1";
    warn "Compute: $cmd\n";
    my $rc = system($cmd);
    if ($rc != 0)
    {
	&fatal("$app computation failed with rc=$rc");
    }
}

$meta->add_log_entry($0, "finish psort computation on $jobdir");
$meta->set_metadata("status.psort", "complete");
exit(0);

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

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

    croak "$0: $msg";
}
    

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