GotCloud: Configuration

The GotCloud configuration file contains the run-time options, including software binaries and command line arguments. A default configuration file is automatically loaded. Users may specify their own configuration file specifying just the values different than the defaults. The configuration file is not required if there are no values to override.

• Default GotCloud configuration file is gotcloud/bin/gotcloudDefaults.conf
• Comments begin with a #
• Format: KEY = value
  • where KEY is the item being set and value is its new value
• Some settings can be defined both in the configuration file and on the GotCloud command-line
  • command-line options take priority over configuration file settings

Reference/Resource Files

• See GotCloud: Genetic Reference and Resource Files for reference/resource file configuration settings

Cluster Configuration Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it. GotCloud will launch the maximum number of jobs in parallel, and wait until one finishes before sending another job to the cluster system.

Configuration Key	Command-line Flag	Value Description
BATCH_TYPE	--batchtype	type of cluster system
		Valid Values	Command to Launch	Command to Check for Completion
		mosix	mosbatch -E/tmp	N/A - interactive type
		sge	qsub	qstat -u $USER
		sgei	qrsh -now n	N/A - interactive type
		pbs	qsub	qstat -u $USER
		slurm	sbatch	squeue -u $USER
		slurmi		N/A - interactive type
		local	N/A - local command	N/A - interactive type
BATCH_OPTS	--batchopts	options to pass to your cluster type, example: -j36,37,38,39,40,41,45,46,47,48,49