Shell Programming and Scripting

I have a very simple script here who's output is supposed to be a text file containing the same command applied to different files. Here it is:

#!/bin/bash
for f1 in newEN*bloc
do
cd ./$f1
for f2 in *.maf
do
awk '{print '"run_lrt.sh /home/awknerd/idea/TEST/$f1/$f2"'}' > /home/awknerd/idea/TEST/mylist.txt
done
cd ..
done


Desired Output:

run_lrt.sh /home/awknerd/idea/TEST/valueoff1/valueoff2


And this line over and over until it reads all values of f1 and f2.

Let's say the value of f2 is worst.maf. I keep getting a syntax error on every line pointing to the ".sh" in "run_lrt.sh" and the ".maf" in the value of file f2. How am I misusing the print command here? Any help would be greatly appreciated. THanks!

You're misusing quotes rather than the print command, try this:

Code:

awk 'BEGIN{print "run_lrt.sh /home/awknerd/idea/TEST/'$f1/$f2'"}' > /home/awknerd/idea/TEST/mylist.txt

ETA: Need a BEGIN clause to run your code as you are not supplying any input file or stdin.