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}
args
$c->{args}
To install Bio::Grid::Run::SGE, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Grid::Run::SGE
CPAN shell
perl -MCPAN -e shell install Bio::Grid::Run::SGE
For more information on module installation, please visit the detailed CPAN module installation guide.