Configuration

Options

Reseved configuration options

Here is a list of reserved configuration options:

  $c = {
    cmd => ...,
    script_dir => ...
    no_post_task => ...,
    tmp_dir => ...,
    stderr_dir => ...,
    stdout_dir => ...,
    result_dir => ...,
    log_dir => ...,
    idx_dir => ...,
    test => ...,
    mail => ...,
    smtp_server => ...,
    no_prompt => ...,
    lib => ...,
    input => ...,
    extra => ...,
    parts => ...,
    combinations_per_job => ...,
    job_name => ...,
    job_id => ...,
    mode => ...,
    _worker_config_file => ...,
    _worker_env_script => ...,
    submit_bin => ...,
    submit_params => ...,
    perl_bin => ...,
    working_dir => ...,
    iterator => ...,

    args => ...,
  };

The attribute args is special, normally the main executable is hard-coded in the cl_* script, but the arguments are changing per configuration. Therefore Bio::Grid::Run::SGE::Master provides the convenience attribute $c->{args}