GotCloud: Configuration

From Genome Analysis Wiki
Jump to: navigation, search

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
  • A KEY can be used in another KEY's value by specifying $(KEY)
    • Example:
      KEY1 = value1
      KEY2 = $(KEY1)/value2
      • When KEY2 is used, it will be equal to: value1/value2

Output Directory

  • The output directory is required for running GotCloud, so GotCloud knows where to write its output
Configuration Key Command-line Flag Value Description
OUT_DIR --outdir output directory

Reference/Resource Files

Cluster Configuration

Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it.

  • For any BATCH_TYPEs that run in batch mode, GotCloud generates a script that will wait until the step is complete before returning
    • In a sense, it "fakes" interactive mode for all batch types since it will not proceed until a command is finished
  • If you are at UM and are using flux, you can specify either flux or pbs
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: