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#! /bin/bash
hipName="$(grep -m 1 "alignmentname=" $1 | cut -d= -f2)"
if [ -z "$hipName" ]
then
echo "Value for 'alignmentname' not found in template. Please check your submission template."
else
nohup ./$1 >> ../$hipName.log 2>&1 &
echo $hipName $! >> ../pid.nohup
echo "Please follow the log in '../$hipName.log'. To track progress live, use 'tail -f ../$hipName.log'."
echo "The nohup job PID is appended to '../pid.nohup' in case the submission should be killed."
echo "You can also use 'ps -ef | grep submit_' to find PIDs of currently running alignments."
fi
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