MyConfig.pm

#
#===============================================================================
#
#         FILE:  MyConfig.pm
#
#  DESCRIPTION:  Package to work space configuration
#         BUGS:  ---
#        NOTES:  ---
#       AUTHOR:  Chaolin Zhang (cz), czhang@rockefeller.edu
#      COMPANY:  Rockefeller University
#      VERSION:  1.0
#      CREATED:  11/22/2004
#     REVISION:  ---
#===============================================================================


package MyConfig;

require Exporter;

our $VERSION = 1.02;

@ISA = qw (Exporter);

@EXPORT = qw (
	getDefaultCache
	getGenomeDir
);


use strict;
use warnings;




=head1 Bed

Subroutines to handle workspace 

=cut

use Carp;


my $user = `whoami`;
chomp $user;
my $projHome = $ENV {"HOME"} . "/scratch";
$projHome = $ENV {"PROJDIR"} if exists $ENV{"PROJDIR"};

sub getDefaultCache
{
	my $base = "cache";
   	$base = $_[0] if (@_ > 0);
	
	my $cacheHome = ".";
	$cacheHome = $ENV{'CACHEHOME'} if exists $ENV{'CACHEHOME'};
	my $cache = "$cacheHome/$base" . "_" . time() . "_" . rand();
	return $cache;
}


sub getDefaultTmpDir
{
	return getDefaultCache (@_);
}


sub getGenomeDir
{
	my $species =$_[0];
	my $genomeDir = "/ifs/data/c2b2/cz_lab/genomes";
	$genomeDir = $ENV{'DATADIR'} . "/genomes" unless -d $genomeDir;

	#cz: please do not change this default dir
	
	my $path = "$genomeDir/$species";
	Carp::croak "can not find the directory for $species: $path\n" unless -d $path;
	
	return $path;

=obsolete
	return "$genomeDir/mm5"	if ($species eq 'mm5');
	return "$genomeDir/mm6" if ($species eq 'mm6');
	return "$genomeDir/mm8" if ($species eq 'mm8');
	return "$genomeDir/mm9" if ($species eq 'mm9');
	return "$genomeDir/mm10" if ($species eq 'mm10');
	return "$genomeDir/hg17" if ($species eq 'hg17');
	return "$genomeDir/hg18" if ($species eq 'hg18');
	return "$genomeDir/hg19" if ($species eq 'hg19');
	return "$genomeDir/hg38" if ($species eq 'hg38');
	return "$genomeDir/panTro3" if ($species eq 'panTro3');
	return "$genomeDir/panTro4" if ($species eq 'panTro4');
	return "$genomeDir/papAnu2" if ($species eq 'papAnu2');
	return "$genomeDir/calJac3" if ($species eq 'calJac3');
	return "$genomeDir/saiBol1" if ($species eq 'saiBol1');
	return "$genomeDir/micMur1" if ($species eq 'micMur1');
	return "$genomeDir/ponAbe2" if ($species eq 'ponAbe2');
	return "$genomeDir/gorGor3" if ($species eq 'gorGor3');
	return "$genomeDir/rheMac2" if ($species eq 'rheMac2');
	return "$genomeDir/rheMac3" if ($species eq 'rheMac3');
	return "$genomeDir/monDom5" if ($species eq 'monDom5');
	return "$genomeDir/ornAna1" if ($species eq 'ornAna1');
	return "$genomeDir/rn4" if ($species eq 'rn4');
	return "$genomeDir/rn5" if ($species eq 'rn5');
	return "$genomeDir/bosTau7" if ($species eq 'bosTau7');
	return "$genomeDir/galGal4" if ($species eq 'galGal4');
	return "$genomeDir/danRer4" if ($species eq 'danRer4');
	return "$genomeDir/xenTro3" if ($species eq 'xenTro3');
	return "$genomeDir/dm6" if ($species eq 'dm6');
	return "$genomeDir/dm2" if ($species eq 'dm2');
	return "$genomeDir/ce2" if ($species eq 'ce2');
	return "$genomeDir/sacCer1" if ($species eq 'sacCer1');
	return "$genomeDir/danRer10" if ($species eq 'danRer10');
	Carp::croak "can not find the directory for $species\n";
=cut
}

1;