Configuration

Options

Reseved configuration options

Example configuration:

'stdout_dir' => '/WORKING_DIR/xml_munge1.tmp/out',
'test'       => '1',
'no_prompt'  => undef,
'input'      => [
  {
    'elements' => [
      '../../2013-10-13_string_b2g_blast/cafa_b2g_blastSTRING_9606_protein.sequences.result/cafa_b2g_blastSTRING_*_protein.sequences.*.blast.gz'
    ],
    'format'   => 'FileList',
    'idx_file' => '/WORKING_DIR/idx/xml_munge1.0.idx'
  }
],
'mode'          => 'Consecutive',
'range'         => [ '1', '1' ],
'submit_bin'    => 'qsub',
'submit_params' => [],
'args'          => [],
'working_dir'   => '/WORKING_DIR/test',
'num_comb'      => 564,
'log_dir'       => '/WORKING_DIR/xml_munge1.tmp/log',
'stderr_dir'    => '/WORKING_DIR/xml_munge1.tmp/err',
'tmp_dir'       => '/WORKING_DIR/xml_munge1.tmp',
'smtp_server'   => 'net.wur.nl',
'job_name'      => 'xml_munge1',
'extra'         => { 'map' => '../split_test.map.json.gz' },
'mail'          => 'joachim.bargsten@wur.nl',
'script_dir'    => '/WORKING_DIR/bin',
'idx_dir'       => '/WORKING_DIR/idx',
'job_cmd' =>
  'qsub -t 1-1 -S perl -N xml_munge1 -e /WORKING_DIR/xml_munge1.tmp/err -o /WORKING_DIR/xml_munge1.tmp/out /WORKING_DIR/xml_munge1.tmp/env.xml_munge1.pl WORKING_DIR/bin/cl_xml_munge.pl --worker /WORKING_DIR/xml_munge1.tmp/xml_munge1.config.dat',
'job_id' => '325541.1',
'cmd'    => [ '/WORKING_DIR/bin/cl_xml_munge.pl' ],
'_worker_config_file' =>
  '/WORKING_DIR/xml_munge1.tmp/xml_munge1.config.dat',
'prefix_output_dirs' => '1',
'perl_bin'           => '/home/cafa/perl5/perlbrew/perls/perl-5.16.3/bin/perl',
'result_dir'         => '/WORKING_DIR/xml_munge1.result',
'part_size'          => 1,
'parts'              => 564

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}