BioSAILs-Command

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META.json  view on Meta::CPAN

            "BioX::Workflow::Command::new" : "0",
            "BioX::Workflow::Command::run" : "0",
            "HPC::Runner::Command" : "0",
            "HPC::Runner::Command::execute_array" : "0",
            "HPC::Runner::Command::execute_job" : "0",
            "HPC::Runner::Command::submit_jobs" : "0",
            "Moose" : "0",
            "MooseX::App" : "1.39",
            "MooseX::App::Command" : "0",
            "MooseX::App::Plugin::Version::Command" : "0",
            "namespace::autoclean" : "0",
            "perl" : "v5.10.0",
            "strict" : "0",
            "utf8" : "0",
            "warnings" : "0"
         }
      },
      "test" : {
         "requires" : {
            "File::Spec::Functions" : "0",
            "FindBin" : "0",

META.yml  view on Meta::CPAN

  BioX::Workflow::Command::new: '0'
  BioX::Workflow::Command::run: '0'
  HPC::Runner::Command: '0'
  HPC::Runner::Command::execute_array: '0'
  HPC::Runner::Command::execute_job: '0'
  HPC::Runner::Command::submit_jobs: '0'
  Moose: '0'
  MooseX::App: '1.39'
  MooseX::App::Command: '0'
  MooseX::App::Plugin::Version::Command: '0'
  namespace::autoclean: '0'
  perl: v5.10.0
  strict: '0'
  utf8: '0'
  warnings: '0'
resources:
  bugtracker: https://github.com/biosails/BioSAILs-Command/issues
  homepage: https://github.com/biosails/BioSAILs-Command
  repository: https://github.com/biosails/BioSAILs-Command.git
version: '1.0'
x_generated_by_perl: v5.22.0

lib/BioSAILs/Command/add.pm  view on Meta::CPAN

package BioSAILs::Command::add;
use v5.10;
use strict;
use warnings FATAL => 'all';
use MooseX::App::Command;
use namespace::autoclean;

extends 'BioX::Workflow::Command::add';

command_short_description 'Add rules to an existing workflow.';
command_long_description 'Add rules to an existing workflow.';

__PACKAGE__->meta->make_immutable;

1;

lib/BioSAILs/Command/execute_array.pm  view on Meta::CPAN

package BioSAILs::Command::execute_array;
use v5.10;
use strict;
use warnings FATAL => 'all';
use MooseX::App::Command;
use namespace::autoclean;

extends 'HPC::Runner::Command::execute_array';

command_short_description 'Execute commands';
command_long_description
    'Take the parsed files from biosails submit_jobs and executes the code';

1;

lib/BioSAILs/Command/execute_job.pm  view on Meta::CPAN

package BioSAILs::Command::execute_job;
use v5.10;
use strict;
use warnings FATAL => 'all';
use MooseX::App::Command;
use namespace::autoclean;

extends 'HPC::Runner::Command::execute_job';

command_short_description 'Execute commands';
command_long_description
    'Take the parsed files from biosails submit_jobs and executes the code';

1;

lib/BioSAILs/Command/get_help.pm  view on Meta::CPAN

use strict;
use warnings;
package BioSAILs::Command::get_help;

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

command_short_description 'A few helper urls';

sub execute {
    my $self = shift;
    my $envelope;
    my $biosails = BioSAILs::Command->new();

    #General
    $envelope = $self->render_message(

lib/BioSAILs/Command/new.pm  view on Meta::CPAN

package BioSAILs::Command::new;
use v5.10;
use strict;
use warnings FATAL => 'all';
use MooseX::App::Command;
use namespace::autoclean;

extends 'BioX::Workflow::Command::new';
command_short_description 'Create a new workflow.';
command_long_description 'Create a new workflow.';

__PACKAGE__->meta->make_immutable;

1;

lib/BioSAILs/Command/render.pm  view on Meta::CPAN

package BioSAILs::Command::render;

use v5.10;
use strict;
use warnings FATAL => 'all';
use MooseX::App::Command;
use namespace::autoclean;

extends 'BioX::Workflow::Command::run';

command_short_description 'Render your workflow.';
command_long_description
    'Render your workflow to a shell script, process the variables, and create all your directories.';

__PACKAGE__->meta->make_immutable;

1;

lib/BioSAILs/Command/submit_jobs.pm  view on Meta::CPAN

package BioSAILs::Command::submit_jobs;

use v5.10;
use strict;
use warnings FATAL => 'all';
use MooseX::App::Command;
use namespace::autoclean;

extends 'HPC::Runner::Command::submit_jobs';

command_short_description 'Submit jobs to the HPC system';
command_long_description 'This job parses your input file and writes out one or
more templates to submit to the scheduler of your choice (SLURM, PBS, etc)';

__PACKAGE__->meta->make_immutable;

1;

lib/BioSAILs/Command/version.pm  view on Meta::CPAN

package BioSAILs::Command::version;

use v5.10;
use strict;
use warnings FATAL => 'all';
use MooseX::App::Command;
use namespace::autoclean;

use BioX::Workflow::Command;
use HPC::Runner::Command;
use BioSAILs::Command;
use MooseX::App::Plugin::Version::Command;

command_short_description 'Get the versions of BioX::Workflow::Command, HPC::Runner::Command, BioSAILs, and perl';
command_long_description 'Get the versions of BioX::Workflow::Command, HPC::Runner::Command, BioSAILs, and perl.' .
    ' Please be sure to include this information in any tickets.';

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