GotCloud: Configuration
From Genome Analysis Wiki
Jump to navigationJump to searchThe 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 andvalue
is its new value
- where
- 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
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
- 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 |