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Revision 1.3 - (download) (as text) (annotate)
Wed Jan 25 18:58:09 2006 UTC (13 years, 9 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, myrast_rel40, 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, caBIG-05Apr06-00, 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, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.2: +3 -0 lines
add working-on-chunk support

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

use strict;
use FIG;
use JobScheduler;
use Sys::Hostname;

my $usage = "compute_sim_chunk";

#
# If there is work available in the local sim queue, process a chunk.
#
# When we're done, reschedule ourself to run again. This lets other things in the queue get
# a chance to go.
#

my $blast_params = "-FF -m 8 -e 1.0e-5 -p blastp";

my $fig = new FIG;

my($pool, $chunk, $nr_file, $fasta, $out_file) = $fig->get_sim_work();

if (!$pool)
{
    print "No work available!\n";
    exit 0;
}

my $x;
if (($x) = ($fasta =~ /^([^\n]+)/))
{
    print "Got work pool=$pool chunk=$chunk NR=$nr_file\nX=$x out=$out_file\n";
}

my $tmp = "$FIG_Config::temp/tmp.fasta.$$";
open(T, ">$tmp") or die "cannot write tmepfile $tmp: $!\n";
print T $fasta;
close(T);

$fig->sim_work_working($pool, $chunk, hostname(), $$);

my $rc = system("$FIG_Config::ext_bin/blastall $blast_params -i $tmp -d $nr_file > $out_file");
if ($rc != 0)
{
    print "Blast failed with rc=$rc\n";
    unlink($tmp);
    exit 1;
}


#
# It worked. Mark this done, and schedule to run again.
#

print "Blast success\n";
$fig->sim_work_done($pool, $chunk, $out_file);

unlink($tmp);

my $js = JobScheduler->new();
my $job = $js->job_create();

my $spath = $job->get_script_path();
open(my $sfh, ">$spath");
print $sfh <<END;
#!/bin/sh
. $FIG_Config::fig_disk/config/fig-user-env.sh
$FIG_Config::bin/compute_sim_chunk
END

close($sfh);
chmod(0775, $spath);

$job->enqueue();

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