Bio-MUST-Apps-FortyTwo

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META.yml  view on Meta::CPAN

  Bio::MUST::Drivers: '0.193030'
  Bio::MUST::Drivers::Cap3: '0'
  Carp: '0'
  Config::Any: '0'
  Const::Fast: '0'
  File::Basename: '0'
  File::Find::Rule: '0'
  Getopt::Euclid: '0'
  IO::Prompter: '0'
  List::AllUtils: '0'
  Modern::Perl: '0'
  Moose: '0'
  Moose::Role: '0'
  Number::Interval: '0'
  POSIX: '0'
  Parallel::Batch: '0'
  Path::Class: '0'
  Smart::Comments: '0'
  Sort::Naturally: '0'
  Template: '0'
  Term::Completion::Path: '0'

Makefile.PL  view on Meta::CPAN

    "Bio::MUST::Drivers" => "0.193030",
    "Bio::MUST::Drivers::Cap3" => 0,
    "Carp" => 0,
    "Config::Any" => 0,
    "Const::Fast" => 0,
    "File::Basename" => 0,
    "File::Find::Rule" => 0,
    "Getopt::Euclid" => 0,
    "IO::Prompter" => 0,
    "List::AllUtils" => 0,
    "Modern::Perl" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "Number::Interval" => 0,
    "POSIX" => 0,
    "Parallel::Batch" => 0,
    "Path::Class" => 0,
    "Smart::Comments" => 0,
    "Sort::Naturally" => 0,
    "Template" => 0,
    "Term::Completion::Path" => 0,

bin/debrief-42.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: debrief-42.pl
# ABSTRACT: Summarize the results of a 42 metagenomic run
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.ulg.ac.be>

use autodie;
use Modern::Perl '2011';

use Getopt::Euclid qw(:vars);

use File::Basename;
use File::Find::Rule;
use List::AllUtils qw(uniq);
use Path::Class qw(dir file);
use Tie::IxHash;

use Bio::MUST::Core;

bin/forty-two.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: forty-two.pl
# ABSTRACT: The Answer to the Ultimate Question of Phylogenomics
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>

use Modern::Perl '2011';

use Getopt::Euclid qw(:vars);

## no critic (RequireLocalizedPunctuationVars)
BEGIN{
    $ENV{Smart_Comments} = $ARGV_verbosity
        ? join q{ }, map { '#' x (2 + $_) } 1..$ARGV_verbosity
        : q{}
    ;
}

bin/leel.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: leel.pl
# ABSTRACT: The Elite of the Phylogenomic Back-Translators

use Modern::Perl '2011';

use Getopt::Euclid qw(:vars);

## no critic (RequireLocalizedPunctuationVars)
BEGIN{
    $ENV{Smart_Comments} = $ARGV_verbosity
        ? join q{ }, map { '#' x (2 + $_) } 1..$ARGV_verbosity
        : q{}
    ;
}

bin/prune-outliers.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: prune-outliers.pl
# ABSTRACT: Identify and discard outliers based on all-versus-all BLAST searches
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
# CONTRIBUTOR: Loic MEUNIER <loic.meunier@doct.uliege.be>

use Modern::Perl '2011';
use autodie;

use File::Basename;
use File::Find::Rule;
use Getopt::Euclid qw(:vars);
use Path::Class qw(dir file);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:dirs);

bin/yaml-generator-42.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: yaml-generator-42.pl
# ABSTRACT: Interactive or batch generator for 42 YAML config files
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>

# TODO: add support for wordsize (default 3) in BRH phase?
# TODO: optimize vertical spacing in output (very tricky)

use autodie;
use Modern::Perl '2011';

use Smart::Comments '###';
use Getopt::Euclid qw(:vars);

use Template;
use Path::Class qw(dir file);
use Tie::IxHash;
use List::AllUtils qw(mesh);
use File::Basename;
use File::Find::Rule;

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