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Revision 1.1 - (download) (as text) (annotate)
Wed Sep 5 20:59:03 2007 UTC (12 years, 2 months ago) by olson
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, rast_rel_2008_04_23, 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
Rollup of RAST->SEED import stuff.

#
# Merge the processed sims with the last batch of computed sims.
#
# processed sims dir is first flipped into sims.flip
# update_sims2 then used to merge the flipped and delete ids
# that are to be deleted. 
#

use strict;

use Data::Dumper;
use FIG;
use FIG_Config;
use File::Basename;
use File::Copy;
use ImportJob;
use GenomeMeta;
use JobStage;

my $hits_max = 300;

@ARGV == 2 or die "Usage: $0 job-dir sim-dir\n";

my $jobdir = shift;
my $simdir = shift;

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

my $stage = new JobStage('ImportJob', 'merge_sims', $jobdir);

$stage or die "$0: Could not create job object";
my $job = $stage->job();

$stage->log("Running on " . $stage->hostname);

$stage->set_status("running");
$stage->set_running("yes");

$stage->set_qualified_metadata("host", $stage->hostname);

#
# Set TMPDIR to somewhere with lots of space.
#
$ENV{TMPDIR} = $FIG_Config::temp;

my $flipped = "$simdir/sim.flips";

my @cmd = ("$FIG_Config::bin/flip_sims", "$simdir/processed", $flipped);
$stage->log("Running @cmd");
my $rc = system(@cmd);

if ($rc == -1)
{
    $stage->fatal("Flip cmd @cmd failed: $!");
}
elsif ($rc != 0)
{
    $stage->fatal("Flip cmd @cmd failed: rc=$rc");
}

my $merge_dir= "$simdir/merged";
if (-d $merge_dir)
{
    rename($merge_dir, "$merge_dir." . time);
}

@cmd = ("$FIG_Config::bin/update_sims2",
	"$jobdir/peg.synonyms", $hits_max, "$simdir/processed", "$simdir/merged",
	$flipped, "$jobdir/ids.deleted");
$stage->log("Running @cmd");
my $rc = system(@cmd);

if ($rc == -1)
{
    $stage->fatal("Merge cmd @cmd failed: $!");
}
elsif ($rc != 0)
{
    $stage->fatal("Merge cmd @cmd failed: rc=$rc");
}

$stage->log("completed");
$stage->set_running("no");
$stage->set_status("complete");

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