I was talking to my PI (Spencer) and he said there was a way to pass bash shell variables directly into HyPhy on the command line but anything I've tried has not come close to working.  For example, I am trying something along the lines of the following:

count=0
while [ $count -lt something number]
do

hyphymp ./infile [trying to pass $count into HyPhy] > outfile &

let count=$count+1
done

Any help would be greatly appreciated.

Sam

Sergei,

Sorry to bug you about this again but I'm having trouble with this still.  I set a bash file with:

#!/bin/bash
bigcount=191
(echo $bigcount) > HYPHYMP ./null.h

and then the ./null.h with:
fscanf(stdin, "test", bigcount);
fprintf(stdout,test);

However, I keep getting an error of:

./test.sh: line 8: syntax error near unexpected token `./null.h'
./test.sh: line 8: `(echo $bigcount) > HYPHYMP ./null.h '


Does this make sense?  I'm still working on it but any help would be greatly appreciated.

Sam