scheduler.config

#!/bin/bash

## This file sets the qsub variables that are used in the batch system

#Handling of standard error
#{oe,eo,n}. oe merges standard error to standard output, eo merges standard output to standard error, n indicates neither and two separate files will result
ERROR_OUTPUT=oe

# walltime
# by default jobs are submitted to qsub with 12 hours wall time
WALL_T=96:00:00

# mail
# Options for the way job e-mail is handled is flagged with -m within the qsub line
# {a,b,e,n}. a - when job is aborted by PBS, b - when job begins, e - when job terminates
# By default no mail will be sent with SPANDx. Default settings are recommended as SPANDx can spawn a large number of jobs if there are several sequences to be analysed. If mail is desired please change the variables below
# Eg to enable aborted and terminated job e-mail "MAIL=ae" and set ADDRESS=your.email@address.com

MAIL=n
ADDRESS=user@university.edu

## requested cpus for assemblies
# some parts of MGAP (velvet optimiser and ICORN2) can take advantage of multiple cores. Change the ncpus variable to specify the number of cores used in the assembly module of SPANDx 
NCPUS=4
MEM=8000MB