NAME

Bioinfo::PBS - my perl module and CLIs for Biology

VERSION

version 0.1.1

SYNOPSIS

  use Bioinfo::PBS;
  my $para =  {
    cpu => 2,
    name => 'blast',
    cmd => 'ls -alh; pwd',
  };
  my $pbs_obj = Bioinfo::PBS->new($para);
  $pbs_obj->qsub;

DESCRIPTION

This module is created to simplify process of task submitting in PBS system, and waiting for the finish of multiple tasks.

ATTRIBUTES

cpu

cpu number that will apply

name

prefix of output of STANDARD and ERR

cmd

the command that will be submitted to cluster

path

the path that cmd will execute in

job_id

the job id of qsub

priority

the priority during the process of Batch submmit in Queue

METHODS

get_sh

get shell file that will used in qsub

qsub

submit the program to cluster

wait

wait until the program finished in cluster

job_stat

get the status of job. 0 will be return if the job has completed

AUTHOR

Yan Xueqing <yanxueqing621@163.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2017 by Yan Xueqing.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.

cpanm Bioinfo

perl -MCPAN -e shell
install Bioinfo