Bio-MUST-Core

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META.yml  view on Meta::CPAN

  Date::Format: '0'
  Exporter::Easy: '0'
  File::Basename: '0'
  File::Find::Rule: '0'
  File::Spec: '0'
  File::Temp: '0'
  Getopt::Euclid: '0'
  Graphics::ColorNames: '0'
  Graphics::ColorNames::HTML: '0'
  Graphics::ColorNames::WWW: '0'
  HTTP::Request::Common: '0'
  IPC::System::Simple: '0'
  LWP::Protocol::https: '0'
  LWP::Simple: '0'
  LWP::UserAgent: '0'
  List::AllUtils: '0.12'
  List::Compare: '0'
  Modern::Perl: '0'
  Moose: '0'
  Moose::Role: '0'
  Moose::Util::TypeConstraints: '0'

Makefile.PL  view on Meta::CPAN

    "Date::Format" => 0,
    "Exporter::Easy" => 0,
    "File::Basename" => 0,
    "File::Find::Rule" => 0,
    "File::Spec" => 0,
    "File::Temp" => 0,
    "Getopt::Euclid" => 0,
    "Graphics::ColorNames" => 0,
    "Graphics::ColorNames::HTML" => 0,
    "Graphics::ColorNames::WWW" => 0,
    "HTTP::Request::Common" => 0,
    "IPC::System::Simple" => 0,
    "LWP::Protocol::https" => 0,
    "LWP::Simple" => 0,
    "LWP::UserAgent" => 0,
    "List::AllUtils" => "0.12",
    "List::Compare" => 0,
    "Modern::Perl" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "Moose::Util::TypeConstraints" => 0,

Makefile.PL  view on Meta::CPAN

  "Date::Format" => 0,
  "Exporter::Easy" => 0,
  "File::Basename" => 0,
  "File::Find::Rule" => 0,
  "File::Spec" => 0,
  "File::Temp" => 0,
  "Getopt::Euclid" => 0,
  "Graphics::ColorNames" => 0,
  "Graphics::ColorNames::HTML" => 0,
  "Graphics::ColorNames::WWW" => 0,
  "HTTP::Request::Common" => 0,
  "IPC::System::Simple" => 0,
  "LWP::Protocol::https" => 0,
  "LWP::Simple" => 0,
  "LWP::UserAgent" => 0,
  "List::AllUtils" => "0.12",
  "List::Compare" => 0,
  "Modern::Perl" => 0,
  "Moose" => 0,
  "Moose::Role" => 0,
  "Moose::Util::TypeConstraints" => 0,

bin/export-itol.pl  view on Meta::CPAN

# ABSTRACT: Download formatted trees from iTOL
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@uliege.be>

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

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

use Config::Any;
use HTTP::Request::Common;
use LWP::UserAgent;

use Bio::MUST::Core;
use Bio::MUST::Core::Constants qw(:files);
use Bio::MUST::Core::Utils qw(change_suffix insert_suffix);


my $download_url = "https://itol.embl.de/batch_downloader.cgi";

my $suffix_like = qr{ \bsvg\b | \bpdf\b | \beps\b | \bps\b | \bpng\b

bin/import-itol.pl  view on Meta::CPAN

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

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

use Archive::Zip qw(:ERROR_CODES :CONSTANTS);
use File::Basename;
use File::Find::Rule;
use HTTP::Request::Common;
use LWP::UserAgent;


my $upload_url = "https://itol.embl.de/batch_uploader.cgi";

# optionally setup tree id outfile
my $out;
if ($ARGV_tree_id_out) {
    open $out, '>', $ARGV_tree_id_out;
    say {$out} '# ' . join "\t", qw ( file id );