EGGeneric.md

EGGeneric

Module: Bio::EnsEMBL::EGPipeline::PipeConfig::EGGeneric_conf.

This is a EGPipeline's base class, used as a generic configuration by the other pipelines. Contains predefined resource classes and a few options shared by other pipelines.

option	default value	meaning
-pipeline_tag		Added by some pipelines as a suffix to the eHive pipeline dbs upon creation
-queue_name		Default LSF queue name
-email		Default email to use

make_resources

This method creates resource strings for LSF and SLURM, to avoid hardcoding them.

It accepts one hashref with the following keys:

option	default value	meaning
queue		Name of the queue/partition
memory		Memory to reserve in MB
time		Time limit in the form 0:00:00 (h:mm:ss)
cpus	1	number of cores
temp_memory	0	Temp memory to reserve
lsf_param	''	A string for specific LSF parameters
slurm_param	''	A string for specific SLURM parameters