Commit 6bee7453 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct auto setup and exit

parent 79979163
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+5 −3
Original line number Diff line number Diff line
@@ -775,7 +775,7 @@ umiadjust=`echo $(($umilength-$umi_default))`
#set up .lock file
if [[ ! -f $lockfile ]]; then
    echo "creating .lock file"
    echo 1 > $lockfile
    echo 0 > $lockfile
    lock=`cat $lockfile`
else
    #check if jobs are running (check value in .lock file)
@@ -794,7 +794,7 @@ else
                echo " call accepted: no conflict detected with other jobs currently running"
                #add current job to lock
                lock=$(($lock+1))
                if [[ $setup == false ]]; then 
                if [[ $setup == "false" ]]; then 
                    echo $lock > $lockfile
                fi
            else
@@ -937,8 +937,10 @@ if [[ $lock -eq 1 ]]; then
    cd - > /dev/null
    
    echo "setup complete"
    if [[ $setup == "true" ]]; then
        exit 0
    fi
fi
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