BioX-Workflow-Command

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META.json  view on Meta::CPAN

            "Path::Tiny" : "0",
            "Safe" : "0",
            "Storable" : "0",
            "String::Approx" : "0",
            "Template::Mustache" : "0",
            "Template::Mustache::Trait" : "0",
            "Text::ASCIITable" : "0",
            "Text::CSV::Slurp" : "0",
            "Text::Template" : "0",
            "Time::localtime" : "0",
            "Try::Tiny" : "0",
            "YAML" : "0",
            "namespace::autoclean" : "0",
            "perl" : "v5.10.0",
            "strict" : "0",
            "utf8" : "0",
            "warnings" : "0"
         }
      },
      "test" : {
         "requires" : {

META.yml  view on Meta::CPAN

  Path::Tiny: '0'
  Safe: '0'
  Storable: '0'
  String::Approx: '0'
  Template::Mustache: '0'
  Template::Mustache::Trait: '0'
  Text::ASCIITable: '0'
  Text::CSV::Slurp: '0'
  Text::Template: '0'
  Time::localtime: '0'
  Try::Tiny: '0'
  YAML: '0'
  namespace::autoclean: '0'
  perl: v5.10.0
  strict: '0'
  utf8: '0'
  warnings: '0'
resources:
  bugtracker: https://github.com/biosails/BioX-Workflow-Command/issues
  homepage: https://github.com/biosails/BioX-Workflow-Command
  repository: https://github.com/biosails/BioX-Workflow-Command.git

lib/BioX/Workflow/Command/Utils/Files.pm  view on Meta::CPAN

package BioX::Workflow::Command::Utils::Files;

use MooseX::App::Role;
use namespace::autoclean;

use MooseX::Types::Path::Tiny qw/AbsFile/;
use File::Basename;
use DateTime;
use Try::Tiny;
use Config::Any;
use File::Spec;

option 'workflow' => (
    is            => 'rw',
    isa           => AbsFile,
    required      => 1,
    coerce        => 1,
    documentation => 'Supply a workflow',
    cmd_aliases   => ['w'],

lib/BioX/Workflow/Command/inspect.pm  view on Meta::CPAN

package BioX::Workflow::Command::inspect;

use v5.10;
use MooseX::App::Command;
use namespace::autoclean;

use Data::Dumper;
use YAML;
use Storable qw(dclone);
use Try::Tiny;
use JSON;

extends 'BioX::Workflow::Command';
use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use Capture::Tiny ':all';

with 'BioX::Workflow::Command::run::Rules::Directives::Walk';
with 'BioX::Workflow::Command::run::Utils::Samples';
with 'BioX::Workflow::Command::run::Utils::Attributes';
with 'BioX::Workflow::Command::run::Rules::Rules';

lib/BioX/Workflow/Command/run/Rules/Directives.pm  view on Meta::CPAN

with 'BioX::Workflow::Command::run::Rules::Directives::Types::CSV';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Glob';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Config';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Mustache';
with 'BioX::Workflow::Command::run::Rules::Directives::Interpolate';
with 'BioX::Workflow::Command::run::Rules::Directives::Functions';
with 'BioX::Workflow::Command::run::Rules::Directives::Sample';
with 'BioX::Workflow::Command::run::Rules::Directives::Walk';
with 'BioX::Workflow::Command::Utils::Log';

use Try::Tiny;

=head2 Other Directives

=cut

has '_ERROR' => (
    is      => 'rw',
    default => 0,
);

lib/BioX/Workflow/Command/run/Rules/Directives/Functions.pm  view on Meta::CPAN

package BioX::Workflow::Command::run::Rules::Directives::Functions;

use MooseX::App::Role;
use namespace::autoclean;

use File::Slurp;
use JSON;
use Try::Tiny;

has 'remove_from_json' => (
    is      => 'rw',
    isa     => 'ArrayRef',
    default => sub {
        [
            'remove_from_json', 'register_namespace',
            '_ERROR',           'register_process_directives',
            'register_types',   'run_stats',
            'interpol_directive_cache', 'before_meta',

lib/BioX/Workflow/Command/run/Rules/Directives/Interpolate.pm  view on Meta::CPAN

package BioX::Workflow::Command::run::Rules::Directives::Interpolate;

use Moose::Role;
use namespace::autoclean;

use Moose::Util qw/apply_all_roles/;

use Try::Tiny;

has 'interpol_directive_cache' => (
    is      => 'rw',
    isa     => 'HashRef',
    default => sub { {} },
);

#TODO This should not be here
has 'before_meta' => (
    traits    => ['String'],

lib/BioX/Workflow/Command/run/Rules/Directives/Interpolate/Jinja.pm  view on Meta::CPAN

use strict;
use warnings;
package BioX::Workflow::Command::run::Rules::Directives::Interpolate::Jinja;

use Moose::Role;
use namespace::autoclean;

use IPC::Cmd qw[can_run run];
use Try::Tiny;
use Safe;
use Storable qw(dclone);
use File::Spec;
use Memoize;
use File::Basename;
use File::Temp qw/tempfile/;
use File::Slurp;

my $TEMPLATE_ERROR = 0;

lib/BioX/Workflow/Command/run/Rules/Directives/Interpolate/Text.pm  view on Meta::CPAN

package BioX::Workflow::Command::run::Rules::Directives::Interpolate::Text;

use Moose::Role;
use namespace::autoclean;

use Text::Template;
use Try::Tiny;
use Safe;
use Storable qw(dclone);
use File::Spec;
use Memoize;
use File::Basename;

our $c = new Safe;
my $TEMPLATE_ERROR = 0;

has 'delimiter' => (

lib/BioX/Workflow/Command/run/Rules/Directives/Types/Config.pm  view on Meta::CPAN

package BioX::Workflow::Command::run::Rules::Directives::Types::Config;

use Moose::Role;
use namespace::autoclean;

with 'BioX::Workflow::Command::run::Rules::Directives::Types::Roles::File';

use Config::Any;
use Try::Tiny;

after 'BUILD' => sub {
    my $self = shift;

    $self->set_register_types(
        'config',
        {
            builder => 'create_reg_attr',
            lookup  => [
                '.*_json$',  '.*_yaml$', '.*_yml$', '.*_jsn$',

lib/BioX/Workflow/Command/run/Rules/Rules.pm  view on Meta::CPAN

package BioX::Workflow::Command::run::Rules::Rules;

use MooseX::App::Role;
use namespace::autoclean;

use Storable qw(dclone);
#use Data::Merger qw(merger);
use Data::Dumper;
use File::Path qw(make_path remove_tree);
use Try::Tiny;
use Path::Tiny;
use MCE::Map;
use Algorithm::Loops qw(NestedLoops);

use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use MCE::Shared;
use MCE::Shared::Cache;

use BioX::Workflow::Command::run::Rules::Exceptions::KeyDeclaration;
use BioX::Workflow::Command::run::Rules::Exceptions::OneRuleName;

lib/BioX/Workflow/Command/run/Utils/Files/ResolveDeps.pm  view on Meta::CPAN

package BioX::Workflow::Command::run::Utils::Files::ResolveDeps;

use strict;
use warnings FATAL => 'all';
use MooseX::App::Role;
use namespace::autoclean;

use String::Approx 'amatch';
use Algorithm::Dependency::Source::HoA;
use Algorithm::Dependency::Ordered;
use Try::Tiny;
use Path::Tiny;
use Text::ASCIITable;
use Data::Dumper;

option 'auto_deps' => (
    is      => 'rw',
    isa     => 'Bool',
    default => 0,
    documentation =>
      'Create a dependency tree using the INPUT/OUTPUTs of a rule',

lib/BioX/Workflow/Command/stats.pm  view on Meta::CPAN

use MooseX::App::Command;
use namespace::autoclean;

use Log::Log4perl qw(:easy);
use DateTime;
use Text::ASCIITable;
use Number::Bytes::Human qw(format_bytes parse_bytes);
use File::Details;
use File::Basename;
use List::Util qw(uniq);
use Try::Tiny;
use Path::Tiny;

extends qw(  BioX::Workflow::Command );

use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);

use BioX::Workflow::Command::run::Rules::Directives;

with 'BioX::Workflow::Command::Utils::Log';
with 'BioX::Workflow::Command::run::Utils::Samples';