A modified qstat wrapper to work with nextflow on QRIS Awoonga

qstat

#!/bin/bash
# put this file in $HOME/bin and make it executable
# make sure that this file is being called by default, I did this by adding `alias "qstat=~/bin/qstat"` to my ~/.bashrc

# Servers
#awoonga="@awongmgmr1.storage:16001 @awonmgr2.storage:16001"
#flashlite="@flm1.ipoib:16001 @flashmgr2.ipoib:16001"
#tinaroo="@tinmgmr1.ib0:16001 @tinmgr2.ib0:16001"
awoonga="@awonmgr2"
flashlite="@flashmgr2"
tinaroo="@tinmgr2"

opts="${*}"
servers="${awoonga} ${flashlite} ${tinaroo}"

TEMP=`getopt -o BD:EF:GHJLMQTafinqrstu:w1 --long version -n 'qstat' -- "$@"`
eval set -- "$TEMP"
# Need to find options that will allow/suppress the wide default
while [ $# -gt 0 ]; do
    case "$1" in
        -B)     opt_B=1; shift ;;
        -Q)     opt_Q=1; shift ;;
        -L)     opt_L=1 ; shift ;;
        -a)     allow_w=1 ; shift ;;
        -n)     allow_w=1 ; shift ;;
        -T)     allow_w=1 ; shift ;;
        -s)     allow_w=1 ; shift ;;
        -f)     allow_w=1 ; opt_f=1; shift ;;
        -q)     deny_w=1 ; shift ;;
        -h)     deny_w=1 ; shift ;;
        -F)     deny_w=1 ; shift ;;
        -D|-F|-u)       shift 2 ;;
        @*)      servers="" ; shift ;;
        *)      shift ;;
    esac
done

# Discover the process tree that invoked us.
ptree=$(/bin/ps -o'comm')

defs=""; wide=""
# If script or terminal sufficiently wide

if [ ${allow_w:-0} -eq 1 ] && [ ${deny_w:-0} -eq 0 ]; then
   if ! /bin/tty -s || [ "$(/bin/tput cols)" -gt 136 ]; then wide="-w"; fi
fi
# this line makes sure that all servers are being queried when using qstat -f
if [ ${opt_f:-0} -eq 1 ]; then
   /bin/timeout --foreground --kill-after=10s 10s /opt/pbs/bin/qstat ${defs} ${opts} ${wide} ${servers}
else

if [ "${opts#-L}" != "${opts}" ] || [ "${opts#-f}" != "${opts}" ]; then

   servers=""
   opts="${opts#-L}"; opts=${opts## }
   if [ "${opts:-x}" != "x" ] && [ "${opts#-}" == "${opts}" ]; then opts="-${opts}"; fi
   /opt/pbs/bin/qstat ${defs} ${opts} ${wide} ${server}
   # Query for all servers - but timeout on no response.

elif [ ${opt_B:-0} -eq 1 ]; then
   # If this is "-B" remove the "@" from servernames
   shopt -s extglob
   if [ "${opts##-B*( )}" != "" ]; then servers=""; fi
   for server in ${servers//@}; do
      /bin/timeout --foreground --kill-after=10s 10s /opt/pbs/bin/qstat ${defs} ${opts} ${server}
   done
elif [ ${opts_Q:-0} -eq 1 ]; then
   # If this is "-Q", need to add server headers
   for server in ${servers}; do
       sname=${server//@}; sname=${sname%:.*}
       /bin/echo -e "\n${sname}\n"
       /bin/timeout --foreground --kill-after=10s 10s /opt/pbs/bin/qstat -Q ${server}
   done
else
   # If script or terminal sufficiently wide
   # Set default view
   if [ "${opts:-x}" == "x" ]; then defs="-1n"; fi
   for server in ${servers}; do
      /bin/timeout --foreground --kill-after=10s 10s /opt/pbs/bin/qstat ${defs} ${opts} ${wide} ${server}
   done
fi
fi
# Delay return if invoked from "watch"
if [ "${ptree}" != "${ptree/watch}" ]; then sleep 20; fi