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.
for file in *.fa
newfile=`echo $file | sed 's/ehed/ehedp/'`
./4s.pl $file > $newfile