run_main.sh

#!/bin/bash
## Bash script that establishes ncap monitoring routines with minimal dependencies on other packages. 
## Load in helper functions. 
execpath="$0"
scriptpath="$(dirname "$execpath")/ncap_utils"
## Get in absolute path loader: 
source "$scriptpath/paths.sh"

## Now declare remote directory name for here and all sourced files: 
set -a
neurocaasrootdir=$(dirname $(get_abs_filename "$execpath"))
userhome="/home/ubuntu"
set +a

source "$scriptpath/workflow.sh"
## Import functions for data transfer 
source "$scriptpath/transfer.sh"

## Now parse arguments in to relevant variables. These will be available to all scripts run from within. 
# Bucket Name  $bucketname
# Group Directory $groupdir 
# Results Directory $resultdir
# Analysis Output Directory $process
# Dataset Name (without path) $dataname
# Dataset Full Path $inputpath (fka $datapath)
# Configuration Name # configname
# Configuration Path # configpath
set -a
parseargsstd "$1" "$2" "$3" "$4"
set +a

echo $bucketname >> "/home/ubuntu/check_vars.txt" 
echo $groupdir >> "/home/ubuntu/check_vars.txt" 
echo $resultdir >> "/home/ubuntu/check_vars.txt" 
echo $processdir >> "/home/ubuntu/check_vars.txt" 
echo $dataname >> "/home/ubuntu/check_vars.txt" 
echo $inputpath >> "/home/ubuntu/check_vars.txt" 
echo $configname >> "/home/ubuntu/check_vars.txt" 
echo $configpath >> "/home/ubuntu/check_vars.txt" 
 
## Set up Error Status Reporting:
errorlog_init 

## Set up STDOUT and STDERR Monitoring:
errorlog_background & 
background_pid=$!
echo $background_pid, "is the pid of the background process"

## MAIN SCRIPT GOES HERE #####################
#bash wait 20 #   "$5" #/home/ubuntu/ncap_remote/run_yass.sh
bash "$5" > "$neurocaasrootdir"/joboutput.txt 2>"$neurocaasrootdir"/joberror.txt
##############################################
## Cleanup: figure out how the actual processing went. 
## MUST BE RUN IMMEDIATELY AFTER PROCESSING SCRIPTS TO GET ERROR CODE CORRECTLY.
errorlog_final

## Once this is all over, send the config and end.txt file
aws s3 cp s3://"$bucketname"/"$configpath" s3://"$bucketname"/"$groupdir"/"$processdir"/$configname
aws s3 cp "$neurocaasrootdir"/update.txt s3://"$bucketname"/"$groupdir"/"$processdir"/
kill "$background_pid"