configure

#!/usr/bin/env perl
##---------------------------------------------------------------------------##
##  File:
##      @(#) configure
##  Author:
##      Robert Hubley <rhubley@systemsbiology.org>
##  Description:
##      Configuration utility for the RepeatModeler package.
##
#******************************************************************************
#* Copyright (C) Institute for Systems Biology 2003-2025 Developed by
#* Arian Smit and Robert Hubley.
#*
#* This work is licensed under the Open Source License v2.1.  To view a copy
#* of this license, visit http://www.opensource.org/licenses/osl-2.1.php or
#* see the license.txt file contained in this distribution.
#*
###############################################################################

=head1 NAME

configure - Configure the RepeatModeler package

=head1 SYNOPSIS

  perl ./configure [options]

=head1 DESCRIPTION

  Interactive configuration script for RepeatModeler.
  Run from inside the RepeatModeler installation directory.

=head1 OPTIONS

=over 4

=item -perlbin <path>

Path to the perl interpreter to embed in script headers.

=item -repeatmasker_dir <path>

Path to the RepeatMasker installation directory.

=item -famdb_dir <path>

Path to the FamDB installation directory (containing famdb.py).

=item -rmblast_dir <path>

Path to the RMBlast bin directory.

=item -rscout_dir <path>

Path to the RepeatScout installation directory.

=item -recon_dir <path>

Path to the RECON installation directory.

=item -repeatafterme_dir <path>

Path to the RepeatAfterMe installation directory.

=item -trf_dir <path>

Path to the directory containing the trf executable.

=item -cdhit_dir <path>

Path to the CD-HIT installation directory.

=item -ucsctools_dir <path>

Path to the UCSC TwoBit tools directory.

=item -genometools_dir <path>

Path to the GenomeTools bin directory (optional, for LTR pipeline).

=item -ltr_retriever_dir <path>

Path to the LTR_Retriever installation directory (optional, for LTR pipeline).

=item -mafft_dir <path>

Path to the MAFFT bin directory (optional, for LTR pipeline).

=item -ninja_dir <path>

Path to the Ninja installation directory (optional, for LTR pipeline).

=item -no_prompt

Non-interactive mode. Never prompts for input. Succeeds silently when all
required values are supplied via command-line options or already configured.
Dies with an error message if any required value is missing or invalid, or
if a partial LTR pipeline specification is supplied.

=back

=head1 SEE ALSO

RepeatModeler

=head1 COPYRIGHT

Copyright 2003-2025 Robert Hubley, Institute for Systems Biology

=head1 AUTHOR

Robert Hubley <rhubley@systemsbiology.org>

=cut

use strict;
use warnings;
use Config;
use Cwd;
use FindBin;
use File::Basename;
use File::Path qw(make_path rmtree);
use File::Spec;
use Getopt::Long;
use Pod::Text;
use lib $FindBin::Bin;
use RepModelConfig;

$| = 1;

my $version     = $RepModelConfig::VERSION;
my $INSTALL_DIR = $FindBin::RealBin;

##
## Command-line option processing
##
my @getopt_args = ( 'version', 'perlbin=s', 'no_prompt' );
push @getopt_args, RepModelConfig::getCommandLineOptions();

my %opts;
Getopt::Long::config( "noignorecase", "bundling_override" );
GetOptions( \%opts, @getopt_args ) or usage();

my $no_prompt = $opts{no_prompt} ? 1 : 0;

if ( $opts{version} ) {
  print "RepeatModeler $version\n";
  exit 0;
}

##
## Must be run from the installation directory
##
if ( getcwd() ne $INSTALL_DIR ) {
  die "\n  ERROR: configure must be run from inside the RepeatModeler\n"
    . "         installation directory:\n\n"
    . "           cd $INSTALL_DIR\n"
    . "           ./configure\n\n";
}

## Apply command-line overrides before any validation
RepModelConfig::resolveConfiguration( \%opts );
my $config = $RepModelConfig::configuration;

##
## Phase 1: Dependency checks (non-interactive)
##
check_dependencies();

##
## Phase 2: Fix perl shebang lines in all RepeatModeler scripts
##
my $perl = resolve_perl( $opts{perlbin} );
update_shebangs( $perl );

##
## Phase 3: Interactive configuration
##
print_banner();

configure_repeatmasker();
configure_famdb();
configure_rmblast();
configure_repeatscout();
configure_recon();
configure_repeatafterme();
configure_trf();
configure_cdhit();
configure_ucsctools();
configure_ltr_pipeline();

##
## Phase 4: Save configuration and summarise
##
RepModelConfig::updateConfigFile();
print_summary();

exit 0;

###########################################################################
## Subroutines
###########################################################################

sub usage {
  my $p = Pod::Text->new( sentence => 0, width => 78 );
  $p->output_fh(*STDOUT);
  $p->parse_file($0);
  exit 1;
}

sub print_banner {
  my $w = 62;
  print "=" x $w . "\n";
  printf " %-*s\n", $w - 2, " RepeatModeler v$version  --  Configuration";
  print "=" x $w . "\n\n";
}

sub section_header {
  my ($title) = @_;
  print "\n" . "-" x 62 . "\n";
  print "  $title\n";
  print "-" x 62 . "\n";
}

sub status_ok   { printf "  [ OK ]  %s\n", $_[0] }
sub status_info { printf "  [    ]  %s\n", $_[0] }
sub status_warn { printf "  [WARN]  %s\n", $_[0] }

##
## Read a line from STDIN, strip newline, return $default if blank.
##
sub prompt {
  my ( $message, $default ) = @_;
  if ( defined $default && $default ne "" ) {
    print "  $message [$default]: ";
  }
  else {
    print "  $message: ";
  }
  my $answer = <STDIN> // "";
  $answer =~ s/[\r\n]+$//;
  return ( $answer eq "" && defined $default ) ? $default : $answer;
}

##
## Prompt for Y/N. Returns 1 for yes, 0 for no.
##
sub prompt_yn {
  my ( $message, $default ) = @_;
  $default //= "n";
  if ( $no_prompt ) {
    return lc($default) eq "y" ? 1 : 0;
  }
  my $hint = ( lc($default) eq "y" ) ? "[Y/n]" : "[y/N]";
  my $answer;
  do {
    print "  $message $hint: ";
    $answer = <STDIN> // "";
    $answer =~ s/[\r\n]+$//;
    $answer = $default if $answer eq "";
  } while ( $answer !~ /^[YyNn]$/i );
  return $answer =~ /^[Yy]$/i ? 1 : 0;
}

##
## Search PATH for an executable. Returns full path or "".
##
sub find_in_path {
  my ($name) = @_;
  for my $dir ( split /:/, ( $ENV{PATH} // "" ) ) {
    my $full = "$dir/$name";
    return $full if -f $full && -x $full;
  }
  return "";
}

##
## Resolve the perl interpreter to use for shebang lines.
##
sub resolve_perl {
  my ($perlbin) = @_;

  my $perl = $^X;

  if ( $perlbin ) {
    if ( -d $perlbin ) {
      for my $candidate ( "$perlbin/perl", "$perlbin/bin/perl" ) {
        if ( -f $candidate && -x $candidate ) {
          $perl = $candidate;
          last;
        }
      }
    }
    elsif ( -f $perlbin && -x $perlbin ) {
      $perl = $perlbin;
    }
    else {
      die "\n  ERROR: -perlbin '$perlbin' does not point to a perl executable.\n\n";
    }
  }

  unless ( File::Spec->file_name_is_absolute($perl) ) {
    $perl = $Config{perlpath} . ( $Config{_exe} // "" );
  }

  die "\n  ERROR: Cannot determine an absolute path for the perl interpreter.\n"
    . "         Try: ./configure -perlbin /path/to/perl\n\n"
    unless File::Spec->file_name_is_absolute($perl) && -x $perl;

  return $perl;
}

##
## Check required Perl modules.
##
sub check_dependencies {
  section_header("Checking Dependencies");

  if ( $] < 5.008 ) {
    printf "  [FAIL]  Perl %s -- version 5.8 or higher is required.\n\n", $];
    exit 1;
  }
  status_ok( "Perl " . sprintf( "%vd", $^V ) );

  my @required = qw( Tie::File Getopt::Long POSIX File::Copy File::Path
                     Data::Dumper Cwd Storable JSON );
  my @missing;
  for my $mod ( @required ) {
    push @missing, $mod unless eval "require $mod; 1";
  }
  if ( @missing ) {
    print "  [FAIL]  Missing Perl modules: " . join( ", ", @missing ) . "\n";
    print "\n  Install via CPAN or your system package manager, "
        . "then re-run configure.\n\n";
    exit 1;
  }
  status_ok("Required Perl modules present");

  unless ( eval "use Scalar::Util qw(weaken); 1" ) {
    print "  [FAIL]  Scalar::Util is not compiled with XS support.\n";
    print "\n  Please reinstall Scalar::Util from CPAN and re-run configure.\n\n";
    exit 1;
  }
  status_ok("Scalar::Util (XS)");
}

##
## Rewrite the perl shebang line in every RepeatModeler script.
##
sub update_shebangs {
  my ($perl) = @_;

  section_header("Perl Interpreter");
  status_ok($perl);

  my @scripts = qw(
    BuildDatabase
    Refiner
    RepeatClassifier
    RepeatModeler
    TRFMask
    LTRPipeline
    util/align.pl
    util/Linup
    util/CntSubst
    util/alignAndCallConsensus.pl
    util/AutoRunBlocker.pl
    util/bestwindow.pl
    util/Blocker.pl
    util/ClusterPartialMatchingSubs.pl
    util/extendFlankingSeqs.pl
    util/extend-stk.pl
    util/fasta-trf-filter.pl
    util/generateSeedAlignments.pl
    util/renameIds.pl
    util/rmblast.pl
    util/TSD.pl
    util/viewMSA.pl
    util/viewMultipleMSA.pl
    util/visualizeAlignPNG.pl
  );

  my $perlEsc = $perl;
  $perlEsc =~ s/\//\\\//g;

  for my $script ( @scripts ) {
    if ( -s $script ) {
      system( qq($perl -i -0pe 's/^#\\!.*perl.*/#\\!$perlEsc/g;' $script) );
    }
  }
}

##
## General helper: configure a required directory-type tool.
## Named args: key, label, desc, url, version_check (optional coderef).
##
sub _configure_dir {
  my (%args) = @_;
  my $key     = $args{key};
  my $label   = $args{label};
  my $opt_key = $config->{$key}->{'command_line_override'};

  section_header($label);
  print "\n  $args{desc}\n";
  print "  $args{url}\n\n" if $args{url};

  # Non-interactive: valid path supplied on command line
  if ( $opts{$opt_key} ) {
    if ( RepModelConfig::validateParam($key) ) {
      status_ok( "$label: " . $config->{$key}->{'value'} );
      $args{version_check}->() if $args{version_check};
      return;
    }
    if ( $no_prompt ) {
      die "\n  ERROR: $label path '$opts{$opt_key}' is not valid.\n"
        . "         Could not find required binaries.\n\n";
    }
    status_warn("Specified $label path is not valid: $opts{$opt_key}");
    print "\n";
  }

  my $current = $config->{$key}->{'value'} // "";

  # Seed from PATH if not currently valid
  if ( !$current || !RepModelConfig::validateParam($key) ) {
    if ( my $binary = ( $config->{$key}->{'expected_binaries'} // [] )->[0] ) {
      my $found = find_in_path($binary);
      $current  = dirname($found) if $found;
    }
  }

  # Offer to keep if already valid
  if ( $current && RepModelConfig::validateParam($key) ) {
    print "  Currently configured: $current\n\n";
    if ( prompt_yn( "Keep this $label configuration?", "y" ) ) {
      status_ok("$label: $current");
      $args{version_check}->() if $args{version_check};
      return;
    }
    print "\n";
  }

  my $expected = join( ", ",
      @{ $config->{$key}->{'expected_binaries'} // [] } );

  while (1) {
    if ( $no_prompt ) {
      die "\n  ERROR: $label is not configured and no -$opt_key was supplied.\n"
        . "         Please specify -$opt_key on the command line.\n\n";
    }
    my $dir = prompt( "Path to $label directory", $current );
    $config->{$key}->{'value'} = $dir;
    if ( RepModelConfig::validateParam($key) ) {
      status_ok("$label: $dir");
      $args{version_check}->() if $args{version_check};
      return;
    }
    print "\n  Could not find required binaries in '$dir'.\n";
    print "  Expected: $expected\n\n" if $expected;
    $current = $dir;
  }
}

##
## Configure RepeatMasker (required).
##
sub configure_repeatmasker {
  _configure_dir(
    key   => 'REPEATMASKER_DIR',
    label => 'RepeatMasker',
    desc  => 'RepeatMasker performs initial masking and is required for '
           . "RepeatModeler's\n  classification pipeline. (4.2.4 or higher)",
    url   => 'https://www.repeatmasker.org/',
    version_check => sub {
      my $val = $config->{'REPEATMASKER_DIR'}->{'value'};
      my $ver = `$val/RepeatMasker -v 2>&1`;
      if ( $ver =~ /version\s+(\d+)\.(\d+)\.(\d+)/ ) {
        my ( $maj, $min, $rev ) = ( $1, $2, $3 );
        unless ( $maj > 4 || ( $maj == 4 && $min > 2 )
              || ( $maj == 4 && $min == 2 && $rev >= 4 ) ) {
          die "\n  ERROR: RepeatMasker $maj.$min.$rev is too old. "
            . "Please use 4.2.4 or higher.\n\n";
        }
        status_info("Version: $maj.$min.$rev");
      }
    },
  );
}

##
## Configure FamDB (required for RepeatClassifier).
##
sub configure_famdb {
  my $key   = 'FAMDB_DIR';
  my $label = 'FamDB';

  section_header("FamDB");
  print "\n  FamDB provides access to the Dfam TE protein and consensus\n";
  print "  libraries used by RepeatClassifier. (V3.0.0 or higher)\n";
  print "  https://github.com/Dfam-consortium/FamDB\n\n";

  my $opt_key = $config->{$key}->{'command_line_override'};

  if ( $opts{$opt_key} ) {
    if ( RepModelConfig::validateParam($key) ) {
      status_ok( "FamDB: " . $config->{$key}->{'value'} );
      return;
    }
    if ( $no_prompt ) {
      die "\n  ERROR: FamDB path '$opts{$opt_key}' is not valid.\n"
        . "         famdb.py must exist and be executable in that directory.\n\n";
    }
    status_warn("Specified FamDB path is not valid: $opts{$opt_key}");
    print "  famdb.py must exist and be executable in that directory.\n\n";
  }

  my $current        = $config->{$key}->{'value'} // "";
  my $currently_valid = $current && RepModelConfig::validateParam($key);

  if ( $currently_valid ) {
    print "  Currently configured: $current\n\n";
    if ( prompt_yn( "Keep this FamDB configuration?", "y" ) ) {
      status_ok("FamDB: $current");
      return;
    }
    print "\n";
  }

  while (1) {
    if ( $no_prompt ) {
      die "\n  ERROR: FamDB is not configured and no -famdb_dir was supplied.\n"
        . "         Please specify -famdb_dir on the command line.\n\n";
    }
    my $dir = prompt(
        "Path to FamDB installation (directory containing famdb.py)",
        $current );
    $config->{$key}->{'value'} = $dir;
    if ( RepModelConfig::validateParam($key) ) {
      status_ok("FamDB: $dir");
      return;
    }
    print "\n  famdb.py not found or not executable in '$dir'.\n\n";
    $current = $dir;
  }
}

##
## Configure RMBlast (required).
##
sub configure_rmblast {
  _configure_dir(
    key   => 'RMBLAST_DIR',
    label => 'RMBlast',
    desc  => 'RMBlast provides the alignment engine for RepeatModeler. '
           . '(2.17.1 or higher)',
    url   => 'https://www.repeatmasker.org/rmblast/',
    version_check => sub {
      my $val = $config->{'RMBLAST_DIR'}->{'value'};
      my $ver = `$val/rmblastn -version 2>&1`;
      if ( $ver =~ /rmblastn:\s+(\d+)\.(\d+)\.(\d+)/ ) {
        my ( $maj, $min, $rev ) = ( $1, $2, $3 );
        unless ( $maj > 2 || ( $maj == 2 && $min > 17 )
              || ( $maj == 2 && $min == 17 && $rev >= 1 ) ) {
          die "\n  ERROR: RMBlast $maj.$min.$rev is too old. "
            . "Please use 2.17.1 or higher.\n\n";
        }
        status_info("Version: $maj.$min.$rev");
      }
    },
  );
}

##
## Configure RepeatScout (required).
##
sub configure_repeatscout {
  _configure_dir(
    key   => 'RSCOUT_DIR',
    label => 'RepeatScout',
    desc  => 'RepeatScout performs de novo repeat discovery. (1.0.7 or higher)',
    url   => 'https://github.com/mmcco/RepeatScout',
    version_check => sub {
      my $val = $config->{'RSCOUT_DIR'}->{'value'};
      my $ver = `$val/RepeatScout -blah 2>&1`;
      if ( $ver =~ /Version\s+(\d+)\.(\d+)\.(\d+)/ ) {
        my ( $maj, $min, $rev ) = ( $1, $2, $3 );
        unless ( $maj > 1 || ( $maj == 1 && $min > 0 )
              || ( $maj == 1 && $min == 0 && $rev >= 7 ) ) {
          die "\n  ERROR: RepeatScout $maj.$min.$rev is too old. "
            . "Please use 1.0.7 or higher.\n\n";
        }
        status_info("Version: $maj.$min.$rev");
      }
    },
  );
}

##
## Configure RECON (required).
##
sub configure_recon {
  _configure_dir(
    key   => 'RECON_DIR',
    label => 'RECON',
    desc  => 'RECON performs automated de novo repeat element definition.',
    url   => 'https://github.com/dfam-consortium/RECON',
  );
}

##
## Configure RepeatAfterMe (required).
##
sub configure_repeatafterme {
  _configure_dir(
    key   => 'REPEATAFTERME_DIR',
    label => 'RepeatAfterMe',
    desc  => 'RepeatAfterMe extends repeat model boundaries. (0.0.7 or higher)',
    url   => 'https://github.com/Dfam-consortium/RepeatAfterMe',
  );
}

##
## Configure TRF (required).
##
sub configure_trf {
  _configure_dir(
    key   => 'TRF_DIR',
    label => 'TRF',
    desc  => 'Tandem Repeat Finder identifies tandem repeats. '
           . 'The executable must be named "trf". (4.0.9 or higher)',
    url   => 'https://github.com/Benson-Genomics-Lab/TRF',
  );
}

##
## Configure CD-HIT (required).
##
sub configure_cdhit {
  _configure_dir(
    key   => 'CDHIT_DIR',
    label => 'CD-HIT',
    desc  => 'CD-HIT clusters sequences to reduce redundancy.',
    url   => 'https://github.com/weizhongli/cdhit',
  );
}

##
## Configure UCSC TwoBit tools (required).
##
sub configure_ucsctools {
  _configure_dir(
    key   => 'UCSCTOOLS_DIR',
    label => 'UCSC TwoBit Tools',
    desc  => 'UCSC TwoBit tools (twoBitToFa, faToTwoBit, twoBitInfo) '
           . 'handle 2bit genome files.',
    url   => 'https://hgdownload.soe.ucsc.edu/admin/exe/',
  );
}

##
## Optionally configure the LTR structural identification pipeline.
##
sub configure_ltr_pipeline {
  section_header("LTR Structural Identification Pipeline  (optional)");

  my @ltr_keys   = qw( GENOMETOOLS_DIR LTR_RETRIEVER_DIR MAFFT_DIR NINJA_DIR );
  my @ltr_opts   = qw( genometools_dir ltr_retriever_dir mafft_dir ninja_dir );
  my @ltr_labels = ( 'GenomeTools', 'LTR_Retriever', 'MAFFT', 'NINJA' );

  my $n_provided = grep { $opts{$_} } @ltr_opts;

  # Partial specification is always an error
  if ( $n_provided > 0 && $n_provided < 4 ) {
    my @missing = map { "-$ltr_opts[$_]" }
                  grep { !$opts{$ltr_opts[$_]} } 0..$#ltr_opts;
    die "\n  ERROR: Partial LTR pipeline specification. "
      . "Supply all four options or none.\n"
      . "  Missing: " . join(", ", @missing) . "\n\n";
  }

  # All four CLI opts provided: validate and configure non-interactively
  if ( $n_provided == 4 ) {
    my @invalid;
    for my $i ( 0..$#ltr_keys ) {
      push @invalid, "  $ltr_labels[$i] (-$ltr_opts[$i]): $opts{$ltr_opts[$i]}"
        unless RepModelConfig::validateParam($ltr_keys[$i]);
    }
    if ( @invalid ) {
      die "\n  ERROR: The following LTR pipeline paths are not valid:\n"
        . join("\n", @invalid) . "\n\n";
    }
    for my $k ( @ltr_keys ) {
      status_ok( "$k: " . $config->{$k}->{'value'} );
    }
    return;
  }

  # None provided: fall back to interactive (or no_prompt auto-default) flow
  print "\n  RepeatModeler can use an LTR structural pipeline to identify\n";
  print "  LTR retrotransposons with greater sensitivity. Requires:\n";
  print "  GenomeTools, LTR_Retriever (v2.9.0), MAFFT, and NINJA.\n\n";

  my $all_valid = !grep { !RepModelConfig::validateParam($_) } @ltr_keys;

  if ( $all_valid ) {
    print "  LTR pipeline currently configured:\n";
    for my $k ( @ltr_keys ) {
      printf "    %-18s  %s\n", $k, $config->{$k}->{'value'};
    }
    print "\n";
    if ( prompt_yn( "Keep this LTR pipeline configuration?", "y" ) ) {
      for my $k ( @ltr_keys ) {
        status_ok( "$k: " . $config->{$k}->{'value'} );
      }
      return;
    }
    print "\n";
  }

  unless ( prompt_yn( "Configure the LTR pipeline?", "n" ) ) {
    status_info("LTR pipeline not configured (optional).");
    return;
  }

  print "\n";

  _configure_dir(
    key   => 'GENOMETOOLS_DIR',
    label => 'GenomeTools',
    desc  => 'GenomeTools provides structural LTR detection (gt ltrharvest).',
    url   => 'http://genometools.org/',
  );

  _configure_dir(
    key   => 'LTR_RETRIEVER_DIR',
    label => 'LTR_Retriever',
    desc  => 'LTR_Retriever identifies and classifies LTR elements. (v2.9.0)',
    url   => 'https://github.com/oushujun/LTR_retriever',
    version_check => sub {
      my $val = $config->{'LTR_RETRIEVER_DIR'}->{'value'};
      my $ver = "";
      if ( open( my $fh, "<", "$val/LTR_retriever" ) ) {
        while ( <$fh> ) {
          if ( /^my\s+\$version\s*=\s*"(\S+)"/ ) { $ver = $1; last; }
        }
        close $fh;
      }
      if ( $ver ) {
        unless ( $ver eq "v2.9.0" ) {
          die "\n  ERROR: LTR_Retriever $ver is not the required version. "
            . "Please use v2.9.0.\n\n";
        }
        status_info("Version: $ver");
      }
    },
  );

  _configure_dir(
    key   => 'MAFFT_DIR',
    label => 'MAFFT',
    desc  => 'MAFFT performs multiple sequence alignment.',
    url   => 'https://mafft.cbrc.jp/alignment/software/',
  );

  _configure_dir(
    key   => 'NINJA_DIR',
    label => 'NINJA',
    desc  => 'NINJA performs rapid phylogenetic analysis.',
    url   => 'https://github.com/TravisWheelerLab/NINJA',
  );
}

##
## Extract FamDB libraries and build BLAST databases in Libraries/.
## Called once at configure time so RepeatClassifier can rely on them.
##
## Print a final summary of the installed configuration.
##
sub print_summary {
  my $w = 62;
  print "\n" . "=" x $w . "\n";
  printf " %-*s\n", $w - 2, " Configuration Summary";
  print "=" x $w . "\n\n";

  my @core = (
    [ 'REPEATMASKER_DIR', 'RepeatMasker'   ],
    [ 'FAMDB_DIR',        'FamDB'          ],
    [ 'RMBLAST_DIR',      'RMBlast'        ],
    [ 'RSCOUT_DIR',       'RepeatScout'    ],
    [ 'RECON_DIR',        'RECON'          ],
    [ 'REPEATAFTERME_DIR','RepeatAfterMe'  ],
    [ 'TRF_DIR',          'TRF'            ],
    [ 'CDHIT_DIR',        'CD-HIT'         ],
    [ 'UCSCTOOLS_DIR',    'UCSC TwoBit'    ],
  );

  for my $item ( @core ) {
    my ( $key, $label ) = @$item;
    my $val = $config->{$key}->{'value'} // "";
    if ( $val && RepModelConfig::validateParam($key) ) {
      printf "  %-16s  %s\n", "$label:", $val;
    }
    else {
      printf "  %-16s  (not configured)\n", "$label:";
    }
  }

  # FamDB database details from famdb.py info
  if ( RepModelConfig::validateParam('FAMDB_DIR') ) {
    my $famdb_dir = $config->{'FAMDB_DIR'}->{'value'};
    my $info = `$famdb_dir/famdb.py info 2>/dev/null` // "";
    if ( $info ) {
      my ( $db_name, $db_ver, $db_date, $db_count );
      $db_name  = $1 if $info =~ /^Database\s*:\s*(\S.*)/m;
      $db_ver   = $1 if $info =~ /^Version\s*:\s*(\S.*)/m;
      $db_date  = $1 if $info =~ /^Date\s*:\s*(\S.*)/m;
      $db_count = $1 if $info =~ /^Total consensus sequences present\s*:\s*(\d+)/m;
      $db_count = $1 if !$db_count && $info =~ /^Total HMMs present\s*:\s*(\d+)/m;
      if ( $db_name ) {
        printf "  %-16s  %s %s (%s)\n", "",
            $db_name, $db_ver // "", $db_date // "";
        printf "  %-16s  %s families\n", "",
            _commify($db_count) if $db_count;
      }
    }
  }

  # Optional LTR pipeline tools
  my @ltr_keys = qw( GENOMETOOLS_DIR LTR_RETRIEVER_DIR MAFFT_DIR NINJA_DIR );
  my $any_ltr  = 0;
  for my $k ( @ltr_keys ) {
    $any_ltr = 1 if RepModelConfig::validateParam($k);
  }

  if ( $any_ltr ) {
    my %ltr_labels = (
      GENOMETOOLS_DIR   => 'GenomeTools',
      LTR_RETRIEVER_DIR => 'LTR_Retriever',
      MAFFT_DIR         => 'MAFFT',
      NINJA_DIR         => 'NINJA',
    );
    print "\n  LTR Pipeline:\n";
    for my $k ( @ltr_keys ) {
      if ( RepModelConfig::validateParam($k) ) {
        printf "  %-16s  %s\n", "  $ltr_labels{$k}:", $config->{$k}->{'value'};
      }
    }
  }

  print "\n" . "=" x $w . "\n";
  printf " %-*s\n", $w - 2, " RepeatModeler v$version is configured and ready.";
  print "=" x $w . "\n\n";
}

sub _commify {
  my $n = reverse( $_[0] // 0 );
  $n =~ s/(\d{3})(?=\d)/$1,/g;
  return scalar reverse $n;
}

1;