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}