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Revision 1.2 - (download) (as text) (annotate)
Fri Nov 7 22:42:29 2008 UTC (11 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, 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_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, 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, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24
Changes since 1.1: +138 -1 lines
First working versoin of the peer sims code.

# Request the computation of all-to-all sims between a set of organism directories.

use strict;
use Data::Dumper;
use Carp;
use DB_File;
use strict;
use FIG;
use FIG_Config;
use File::Basename;
use GenomeMeta;
use FileHandle;
use Sim;
use GeneralJob;
use FileLocking qw(lock_file unlock_file);
use SGE;

my $meta;

@ARGV > 0 or die "Usage: $0 job-id job-id ...\n";

my @job_ids = @ARGV;

$FIG_Config::general_jobdir ne '' or die "\$FIG_Config::general_jobdir must be set\n";

my $sge = new SGE;

# First walk the list of jobs we're setting up sims for and touch the
# orgdir/sims/org2.queued file to mark them as queued for computation.

my @jobs;
for my $j (@job_ids)
    my $d = "$FIG_Config::rast_jobs/$j";
    my $g = &FIG::file_head("$d/GENOME_ID", 1);
    $g or die "cannot read jobdir $g";
    chomp $g;
    my $simdir = "$d/rp/$g";

    if (! -d "$simdir/sims")
    if (! -f "$simdir/sims/lock")
	open(LF, ">", "$simdir/sims/lock");

    push(@jobs, [$j, $d, $g, $simdir]);

my %need;

for my $j1idx (0..@jobs-1)
    my($j1_id, $j1_jobdir, $j1_genome, $j1_orgdir) = @{$jobs[$j1idx]};

    # Lock the sims dir while we are doing this check.

    open(LF, "+<", "$j1_orgdir/sims/lock") or die
	"Cannot open lockfile $j1_orgdir/sims/lock: $!";
    for my $j2idx (0..@jobs-1)
	next if $j1idx == $j2idx;
	my($j2_id, $j2_jobdir, $j2_genome, $j2_orgdir) = @{$jobs[$j2idx]};

	my $simfile_base = "$j1_orgdir/sims/$j2_genome";

	print "checking $simfile_base\n";
	if (-f "$simfile_base.queued")
	    print "$j1_genome $j2_genome already queued\n";
	elsif (-f "$simfile_base.in_progress")
	    print "$j1_genome $j2_genome already in progress\n";
	elsif (-f "$simfile_base")
	    print "$j1_genome $j2_genome already computed\n";
	    my($j1, $j2) = sort { $a <=> $b } ($j1idx, $j2idx);


for my $pair (sort keys %need)
    my ($j1idx, $j2idx) = split(/$;/, $pair);
    #my($id, $jobdir, $genome, $orgdir) = @{$jobs[$jidx]};
    #print "Need to compute $id $jobdir $genome $orgdir\n";
    print "need to compute $j1idx $j2idx\n";

    my $jobid = GeneralJob->create_new_job($FIG_Config::general_jobdir);

    my $job = GeneralJob->new($FIG_Config::general_jobdir, $jobid);

    mark_queued($j1idx, $j2idx);

    my $j1 = $jobs[$j1idx]->[0];
    my $j2 = $jobs[$j2idx]->[0];

    my $work = $job->dir;
    mkdir "$work/sge_output";

    my @args = (-N => "p${j1}_${j2}",
		-e => "$work/sge_output",
		-o => "$work/sge_output",
		-v => "PATH",
		-b => "yes",
    my $args = join(" ", @args);

    my $cmd = "$FIG_Config::bin/rp_compute_peer_sim_pair $work $j1 $j2";
    my $jobid = $sge->submit_job($job->meta, $args, $cmd);

    print "Submitted $jobid\n";

sub mark_queued
    my($from, $to) = @_;

    my $g1 = $jobs[$from]->[2];
    my $g2 = $jobs[$from]->[2];

    my $d1 = $jobs[$from]->[1] . "/rp/$g1";
    my $d2 = $jobs[$to]->[1] . "/rp/$g2";

    print "mark $g1  $g2 / $d1 $d2\n";

    -d "$d1/sims" or mkdir "$d1/sims" or die "cannot mkdir $d1/sims: $!";
    if (!open(LF, "+<", "$d1/sims/lock"))
	open(LF, "+>", "$d1/sims/lock") or die
	    "Cannot open lockfile $d1/sims/lock: $!";

    open(S, ">", "$d1/sims/$g2.queued") or die "cannot mark $d1/sims/$g2.queued: $!";

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