view release on metacpan or search on metacpan
"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" : {
"File::Spec::Functions" : "0",
"FindBin" : "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
version: 2.4.1
x_generated_by_perl: v5.22.0
lib/BioX/Workflow/Command/Exceptions.pm view on Meta::CPAN
package BioX::Workflow::Command::Exceptions;
use Moose;
use namespace::autoclean;
has 'message' => (
is => 'rw',
isa => 'Str',
required => 0,
documentation => 'This is a general message for the type of error thrown.',
predicate => 'has_message',
);
has 'info' => (
lib/BioX/Workflow/Command/Utils/Create.pm view on Meta::CPAN
package BioX::Workflow::Command::Utils::Create;
use MooseX::App::Role;
use namespace::autoclean;
use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use Storable qw(dclone);
option 'rules' => (
traits => ['Array'],
is => 'rw',
required => 0,
isa => ArrayRefOfStrs,
documentation => 'Add rules',
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',
lib/BioX/Workflow/Command/Utils/Log.pm view on Meta::CPAN
package BioX::Workflow::Command::Utils::Log;
use Moose::Role;
use namespace::autoclean;
use Log::Log4perl qw(:easy);
use DateTime;
has 'app_log' => (
is => 'rw',
default => sub {
my $self = shift;
Log::Log4perl->init( \ <<'EOT');
log4perl.category = DEBUG, Screen
lib/BioX/Workflow/Command/add.pm view on Meta::CPAN
package BioX::Workflow::Command::add;
use v5.10;
use MooseX::App::Command;
use namespace::autoclean;
use YAML;
extends 'BioX::Workflow::Command';
with 'BioX::Workflow::Command::Utils::Create';
with 'BioX::Workflow::Command::Utils::Files';
with 'BioX::Workflow::Command::Utils::Log';
command_short_description 'Add rules to an existing workflow.';
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';
lib/BioX/Workflow/Command/inspect/Exceptions/Path.pm view on Meta::CPAN
package BioX::Workflow::Command::inspect::Exceptions::Path;
use Moose;
use namespace::autoclean;
extends 'BioX::Workflow::Command::Exceptions';
sub BUILD {
my $self = shift;
$self->message('Path specification is incorrect.');
}
1;
lib/BioX/Workflow/Command/inspect/Utils/ParsePlainText.pm view on Meta::CPAN
package BioX::Workflow::Command::inspect::Utils::ParsePlainText;
use Moose::Role;
use namespace::autoclean;
use File::Slurp;
has 'workflow_plain_text' => (
is => 'rw',
lazy => 1,
default => sub {
my $self = shift;
return read_file( $self->workflow, array_ref => 1 );
}
);
lib/BioX/Workflow/Command/new.pm view on Meta::CPAN
package BioX::Workflow::Command::new;
use v5.10;
use MooseX::App::Command;
use namespace::autoclean;
use Storable qw(dclone);
use YAML;
use MooseX::Types::Path::Tiny qw/Path/;
use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
extends 'BioX::Workflow::Command';
lib/BioX/Workflow/Command/run.pm view on Meta::CPAN
package BioX::Workflow::Command::run;
use v5.10;
use MooseX::App::Command;
use namespace::autoclean;
use File::Path qw(make_path);
extends 'BioX::Workflow::Command';
use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use BioX::Workflow::Command::run::Rules::Directives;
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
package BioX::Workflow::Command::run::Rules::Directives;
use Moose;
use namespace::autoclean;
use Moose::Util qw/apply_all_roles/;
with 'BioX::Workflow::Command::run::Rules::Directives::Types::HPC';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Path';
#with 'BioX::Workflow::Command::run::Rules::Directives::Types::List';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Stash';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Hash';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Array';
with 'BioX::Workflow::Command::run::Rules::Directives::Types::CSV';
lib/BioX/Workflow/Command/run/Rules/Directives/Exceptions/DidNotDeclare.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Exceptions::DidNotDeclare;
use Moose;
use namespace::autoclean;
extends 'BioX::Workflow::Command::Exceptions';
sub BUILD {
my $self = shift;
}
1;
lib/BioX/Workflow/Command/run/Rules/Directives/Exceptions/SyntaxError.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Exceptions::SyntaxError;
use Moose;
use namespace::autoclean;
extends 'BioX::Workflow::Command::Exceptions';
sub BUILD {
my $self = shift;
}
1;
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 {
[
lib/BioX/Workflow/Command/run/Rules/Directives/Inspect.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Inspect;
use Moose::Role;
use namespace::autoclean;
use Data::Dumper;
use Storable qw(dclone);
use YAML;
use BioX::Workflow::Command::run::Rules::Directives::Exceptions::DidNotDeclare;
use BioX::Workflow::Command::run::Rules::Directives::Exceptions::SyntaxError;
with 'BioX::Workflow::Command::inspect::Utils::ParsePlainText';
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 { {} },
);
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;
lib/BioX/Workflow/Command/run/Rules/Directives/Interpolate/Mustache.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Interpolate::Mustache;
use Moose::Role;
use namespace::autoclean;
use Template::Mustache;
has 'delimiter' => (
is => 'rw',
isa => 'Str',
default => '{',
);
has 'sample_var' => (
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;
lib/BioX/Workflow/Command/run/Rules/Directives/Sample.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Sample;
use MooseX::App::Role;
use namespace::autoclean;
use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use MooseX::Types::Path::Tiny qw/Path Paths AbsPath AbsPaths AbsFile/;
=head3 sample_rule
Rule to find files/samples
=cut
lib/BioX/Workflow/Command/run/Rules/Directives/Types/Array.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Types::Array;
use Moose::Role;
use namespace::autoclean;
sub create_ARRAY_attr {
my $self = shift;
my $meta = shift;
my $k = shift;
$meta->add_attribute(
$k => (
# traits => ['Array'],
isa => 'ArrayRef',
lib/BioX/Workflow/Command/run/Rules/Directives/Types/CSV.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Types::CSV;
use Moose::Role;
use namespace::autoclean;
use Text::CSV::Slurp;
with 'BioX::Workflow::Command::run::Rules::Directives::Types::Roles::File';
after 'BUILD' => sub {
my $self = shift;
$self->set_register_types(
'csv',
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(
lib/BioX/Workflow/Command/run/Rules/Directives/Types/Glob.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Types::Glob;
use Moose::Role;
use namespace::autoclean;
use File::Glob;
after 'BUILD' => sub {
my $self = shift;
$self->set_register_types(
'glob',
{
builder => 'create_reg_attr',
lib/BioX/Workflow/Command/run/Rules/Directives/Types/HPC.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Types::HPC;
use Moose::Role;
use namespace::autoclean;
has 'HPC' => (
is => 'rw',
isa => 'HashRef|ArrayRef',
default => sub { {} }
);
# after 'BUILD' => sub {
# my $self = shift;
#
lib/BioX/Workflow/Command/run/Rules/Directives/Types/Hash.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Types::Hash;
use Moose::Role;
use namespace::autoclean;
sub create_HASH_attr {
my $self = shift;
my $meta = shift;
my $k = shift;
$meta->add_attribute(
$k => (
# traits => ['Hash'],
isa => 'HashRef',
lib/BioX/Workflow/Command/run/Rules/Directives/Types/List.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Types::List;
use Moose::Role;
use namespace::autoclean;
=head2 Iterables
DEPRECATED
Use data_loop instead!
Lists to iterate by
Chunks and chroms are included by default
lib/BioX/Workflow/Command/run/Rules/Directives/Types/Mustache.pm view on Meta::CPAN
package BioX::Workflow::Command::run::Rules::Directives::Types::Mustache;
use Moose::Role;
use namespace::autoclean;
use Template::Mustache;
use Template::Mustache::Trait;
use File::Glob;
use File::Basename;
after 'BUILD' => sub {
my $self = shift;
$self->set_register_types(
view release on metacpan - search on metacpan