00_init.sh

#!/bin/bash

#source this script in your .bash_profile:
#  source ~/neuroglia-helpers/00_init.sh 

#if you don't want to see the welcome message, use:
#  source ~/neuroglia-helpers/00_init.sh light



#light version doesn't display welcome message
if [ "$#" = 1 ]
then
	use_light=1
else
	use_light=0
fi

if [ "$use_light" = 0 ]
then

echo "***"
echo " Initializing neuroglia-helpers"

fi

#-------- this section always gets run -------
export NEUROGLIA_DIR=$(dirname `realpath $BASH_SOURCE`)

export PATH=${NEUROGLIA_DIR}/bin:$PATH
export NEUROGLIA_BASH_LIB=$NEUROGLIA_DIR/etc/bash_lib.sh

set -a
source $NEUROGLIA_DIR/cfg/graham${cfg_profile}.cfg
set +a

#make SINGULARITY_DIR if it doesn't exist
if [ ! -e $SINGULARITY_DIR/bids-apps ]
then
	mkdir -p $SINGULARITY_DIR/bids-apps 

	if [ ! "$?" = 0 -o ! -e $SINGULARITY_DIR ]
	then
		echo "neuroglia-helpers init error:  Unable to set local SINGULARITY_DIR to $SINGULARITY_DIR"
	fi

fi


#----------------------------------------------

if [ "$use_light" = 0 ]
then

echo " Container path: $SINGULARITY_DIR"
echo " Singularity options: $SINGULARITY_OPTS"
echo " Neuroglia container: $NEUROGLIA_URI"
echo " CPU account: $CC_COMPUTE_ALLOC"

#echo "- printGroupUsage currently disabled -"
$NEUROGLIA_DIR/etc/printGroupUsage ${CC_COMPUTE_ALLOC}_cpu

echo "***"

fi