amu_run_protocol

#!/bin/bash

[ $AMU_HOME ] || { echo "AMU_HOME not set. Exiting." ; exit ; }

f=$1
num=$2
i=0

[ $f ] || { echo -e "No stack file given. Exiting.\nusage: $(basename $0) <protocol> [num_steps]" ; exit ; }


source $AMU_HOME/ambermd_util.bash

ret="0"
mdin=""
while [[ `amu_protocol_clean $f | wc -l` -gt 0 ]] ; do
r=`amu_protocol_clean $f | head -n 1 | sed 's/#.*$//'`
newmdin=`echo $r  | awk '{print $2}' | sed -e "s/#.*//"` 
r=`echo $r | awk '{print $1}'`
[ $newmdin ] && { mdin=$newmdin ; echo $mdin ; }
if [ ! -d $r ] ; then
    if [ ! $mdin ]; then
        mdin=`tac $f | awk '{print $2}' | tr -d '\t' | sed -e "s/#.*$//" -e "/^[\s\t]*$/d"  | head -n 1`
    fi
    if [ -z $mdin ]; then
            echo "Don't know how to run $r, make it manually, match a mdin file to $r in $f, or provide a previous step with a known mdin file. Exiting."
            exit 1
    fi
    amu_make_step $mdin
fi
[ -f ${f}.log ] && sed -i "/\s\+$r\s/d" ${f}.log
amu_run_step $r | tee >( grep $r >> ${f}.log )

ret=${PIPESTATUS[0]}
[[ $ret -eq 0 ]] || break ;
sed -i "s/^\s*\(\<${r}\>.*\)$/|\1/" $f
i=$(( i+1 ))
if [ ${num} ] && [ "${i}" -eq "${num}" ] ; then break ; fi
sleep 2
done
[[ $ret -eq 0 ]] || echo "Stack failed."
exit $ret