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lib/Bioinfo/App/Cmd/Blast/Cmd/SplitSubmitB.pm  view on Meta::CPAN

package Bioinfo::App::Cmd::Blast::Cmd::SplitSubmitB;
use Modern::Perl;
use Moo;
use MooX::Cmd;
use MooX::Options prefer_commandline => 1;
use IO::All;
use Bioinfo::PBS::Queue;

our $VERSION = '0.1.15'; # VERSION: 
# ABSTRACT: submit blast after splitting a fasta file into multiple files;


option indir => (
  is  => 'ro',
  required  => 1,
  format  => 's',
  short => 'i',
  doc => 'the dir include fasta format file'
);


option split_num => (
  is  => 'ro',
  format  => 'i',
  short => 's',
  default => sub { '20' },
  doc => 'number of files that the fasta file will be split. Default:20'
);


option blast_cpu => (
  is => 'ro',
  format => 'i',
  short => 'c',
  default => sub { '8' },
  doc => 'cpu number will be used by blastp in each node of Cluster.default:8',
);


option parallel_task_num => (
  is => 'ro',
  format => 'i',
  short => 'p',
  default => sub { '20' },
  doc => 'the task number will be running at the same time. default:20',
);


option db => (
  is  => 'rw',
  format => 's',
  short => 'd',
  default => sub { 'nr_plant' },
  doc => 'the database that blast will use, should be absolute path. default:nr_plant',
);


option type => (
  is  => 'rw',
  format => 's',
  short => 't',
  default => sub { 'pbs' },