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Revision 1.3 - (download) (as text) (annotate)
Thu Jan 17 21:31:21 2008 UTC (11 years, 9 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, 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, 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 1.2: +1 -1 lines
checks for PUBLIC file

if(scalar(@ARGV) != 2){
    print "usage: prepare_metagenome_files_for_ftp location_of_jobs_dir ftp_dir\n";
    print "example: prepare_metagenome_files_for_ftp /vol/mg-rast/Jobs.dev /vol/ftp.theseed.org/Metagenomes\n";
    exit;
}

#$jobs_dir is location of jobs to moved to ftp
my $jobs_dir = shift(@ARGV);

#$target_dir is is destination directory to be mirrored to ftp dir 
my $target_dir = shift(@ARGV);

opendir(DIR,"$jobs_dir");
@jobs = readdir(DIR);
close(DIR);

foreach my $job (@jobs){
    $job = 13;
    
    if(! -e "$jobs_dir/$job/PUBLIC"){next}
 
    my $mg_id;
    open(IN,"$jobs_dir/$job/GENOME_ID");
    while($_ = <IN>){
	chomp($_);
	$mg_id = $_;
    }
    close(IN);
    
    if(-e $target_dir/$mg_id.peg.fasta){ 
	if(`cmp $jobs_dir/$job/$mg_id.peg.fasta $target_dir/$mg_id.peg.fasta`){   
	    `cp $jobs_dir/$job/$mg_id.peg.fasta $target_dir/$mg_id.peg.fasta`;
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.peg.fasta $target_dir/$mg_id.peg.fasta`;
    }
    
    if(-e $target_dir/$mg_id.assigned_functions.txt){ 
	if(`cmp $jobs_dir/$job/$mg_id.assigned_functions.txt $target_dir/$mg_id.assigned_functions.txt`){	
	    `cp $jobs_dir/$job/$mg_id.assigned_functions.txt $target_dir/$mg_id.assigned_functions.txt`;
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.assigned_functions.txt $target_dir/$mg_id.assigned_functions.txt`;
    }
    
    if(-e $target_dir/$mg_id.genome_and_proc_dir.tar.gz){
	if(`cmp $jobs_dir/$job/$mg_id.genome_and_proc_dir.tar.gz $target_dir/$mg_id.genome_and_proc_dir.tar.gz`){
	    `cp $jobs_dir/$job/$mg_id.genome_and_proc_dir.tar.gz $target_dir/$mg_id.genome_and_proc_dir.tar.gz`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.genome_and_proc_dir.tar.gz $target_dir/$mg_id.genome_and_proc_dir.tar.gz`; 
    }

    if(-e $target_dir/$mg_id.normalized.fasta){
	if(`cmp $jobs_dir/$job/$mg_id.normalized.fasta $target_dir/$mg_id.normalized.fasta`){ 
	    `cp $jobs_dir/$job/$mg_id.normalized.fasta $target_dir/$mg_id.normalized.fasta`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.normalized.fasta $target_dir/$mg_id.normalized.fasta`; 
    }

    if(-e $target_dir/$mg_id.gbk.gz){
	if(`cmp $jobs_dir/$job/$mg_id.gbk.gz $target_dir/$mg_id.gbk.gz`){ 
	    `cp $jobs_dir/$job/$mg_id.gbk.gz $target_dir/$mg_id.gbk.gz`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.gbk.gz $target_dir/$mg_id.gbk.gz`; 
    }

    if(-e $target_dir/$mg_id.user_id_to_normalized_unique.txt){
	if(`cmp $jobs_dir/$job/$mg_id.user_id_to_normalized_unique.txt $target_dir/$mg_id.user_id_to_normalized_unique.txt`){ 
	    `cp $jobs_dir/$job/$mg_id.user_id_to_normalized_unique.txt $target_dir/$mg_id.user_id_to_normalized_unique.txt`; 
	}
    }
    else{
	`cp $jobs_dir/$job/$mg_id.user_id_to_normalized_unique.txt $target_dir/$mg_id.user_id_to_normalized_unique.txt`; 
    }

} 

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