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Revision 1.2 - (download) (as text) (annotate)
Fri Feb 2 16:42:52 2007 UTC (13 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
Changes since 1.1: +1 -1 lines
use FIG_Config for jobs direcotry(backend)

# Copy the base parts of genome directory into a new job directory in the 48hr server.
# Used for test/debugging.

use strict;
use FIG_Config;
use File::Copy;
use GenomeMeta;

@ARGV > 0 or die "usage: $0 genome [...]\n";

my $job_spool_dir = $FIG_Config::fortyeight_jobs;

opendir(D, $job_spool_dir) or  die "Cannot open job directory $job_spool_dir: $!\n";

my @jobs = sort { $b <=> $a } grep { /^\d+$/ and -d "$job_spool_dir/$_" } readdir(D);

my $next_job;
if (@jobs)
    $next_job = $jobs[0] + 1;
    $next_job = 1;

my %info;
for my $genome (@ARGV)
    my $gp = "$FIG_Config::organisms/$genome";
    -d $gp or die "Genome directory for $genome not found\n";

    my $job = $next_job++;
    my $jobdir = sprintf("$job_spool_dir/%04d", $job);
    -d $jobdir and die "Job directory $jobdir already exists\n";
    $info{$genome} = [$gp, $job, $jobdir];

my @files_to_copy = qw(GENOME PROJECT TAXONOMY);
for my $genome (@ARGV)
    my($gpath, $job, $jobdir) = @{$info{$genome}};

    print "Copy $jobdir from $gpath\n";

    mkdir $jobdir or die "mkdir $jobdir failed: $!\n";
    mkdir "$jobdir/raw" or die "mkdir $jobdir/raw failed: $!\n";
    mkdir "$jobdir/raw/$genome" or die "mkdir $jobdir/raw/$genome failed: $!\n";

    for my $f (@files_to_copy)
	copy("$gpath/$f", "$jobdir/raw/$genome/$f") or die "Cannot copy $gpath/$f to $jobdir/raw/$genome/$f: $!\n";
	copy("$gpath/$f", "$jobdir/$f") or die "Cannot copy $gpath/$f to $jobdir/$f: $!\n";
    system("cp $gpath/contig* $jobdir/raw/$genome/.");
    open(U, ">$jobdir/GENOME_ID") or die "cannot open $jobdir/GENOME_ID: $!\n";
    print U "$genome\n";
    open(U, ">$jobdir/USER") or die "cannot open $jobdir/USER: $!\n";
    print U (getpwuid($>))[0], "\n";

    my $meta = new GenomeMeta($genome, "$jobdir/meta.xml");
    $meta->add_log_entry("genome", "Created $jobdir from $gpath");
    $meta->set_metadata("status.uploaded", "complete");

    open(A, ">$jobdir/ACTIVE") or die "cannot open $jobdir/ACTIVE: $!\n";

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