set max number of loops to wait for file

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13777 ee4ac58c-ac51-4696-9907-e4b3aa274f04

etc/run_blastn.sanger

@@ -86,7 +86,7 @@ run_one_prog () {
     fi
 
     #### end of changes
-    while [ ! -f $OUTPUT_FILE ]; do sleep 2; done
+    count=0; while  (test ! -f $OUTPUT_FILE)  && (test $count -lt 1000) ; do sleep 2; count+=1; done
 
     if [ -s ${PROG}_errors.new ]
     then