rebuild

#!/usr/bin/env perl

#
# Module Dependence
#
use strict;
use Cwd;
use FindBin;
use lib $FindBin::Bin;
use Getopt::Long;
use LibraryUtils;
use RepeatMaskerConfig;

my $rmLocation = "$FindBin::Bin";
print "$rmLocation\n";
my ( $combLib, $tag1, $rmLibraryVersion ) =
    LibraryUtils::validateLibraries( "$rmLocation/Libraries", "CONSENSUS" );

my ( $na, $tag2, $dfamLibraryVersion ) =
    LibraryUtils::validateLibraries( "$rmLocation/Libraries", "HMM" );

print "\n  -- Building FASTA database...";
system(
"$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl > $rmLocation/Libraries/RepeatMasker.lib 2>/dev/null"
);

# Freeze RM and RMPep libraries for RepeatModeler use among others
print "\n  -- Building RMBlast frozen libraries..\n";
system(   "$RepeatMaskerConfig::RMBLASTDB_PRGM -dbtype nucl -in "
        . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
system(   "$RepeatMaskerConfig::RMBLASTDB_PRGM -dbtype prot -in "
        . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );