So Im using our university servers through an ssh connection. I have a bunch of files in a directory which I would like to run through a perl script. So I thought this simple script I concocted should do the trick. I have used similar script on my home computer to do renaming of files (replace last line with mv $file $newfile) and it worked all-right. Alas when I use this on our uni server. Then it will produce error message :

./super: line 4: syntax error near unexpected token `newfile=`echo $file | sed 's/ehed/ehedp/'`'

Is it something to do with me opening a shell inside a remote ssh shell, etc? Should I quote something out even more :D.
Here is the script.

#!/bin/bash
for file in *.fa

newfile=`echo $file | sed 's/ehed/ehedp/'`
./4s.pl $file > $newfile
done

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so,

you're missing the do, in the for var in list; do :....; done

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so,

you're missing the do, in the for var in list; do :....; done

Ahh ... silly me! Thank you!

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