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Old 07-23-2010, 06:20 AM   #6
aleferna
Senior Member
 
Location: sweden

Join Date: Sep 2009
Posts: 121
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Well if all fails here's a simple little script to Multithread any application, I use it whenever I have to use blat or maq which don't have multithread support. It counts how many processes have been started and if there are less than the number of threads (24 in the script below) it starts a new one. All you need to do is cut your reads into many pieces.


for x in *.fa
do

while [ $(ps -Af | grep "blast" | wc -l) -gt 24 ]
do
sleep 5
done

blast $x &...
sleep 1

done
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