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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> Passing bash variables to HyPhy on the command line http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1327461898 Message started by SamW on Jan 24^th, 2012 at 7:24pm

Title: Passing bash variables to HyPhy on the command line
Post by SamW on Jan 24^th, 2012 at 7:24pm

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

Title: Re: Passing bash variables to HyPhy on the command line
Post by Sergei on Jan 24^th, 2012 at 8:24pm

Hi Sam,

Try

Code (]
(echo $count) > HYPHYMP ./infile
[/code):

in the shell script and then

[code]
fscanf (stdin, "Number", count);

in "infile"

Sergei

Title: Re: Passing bash variables to HyPhy on the command line
Post by SamW on Jan 26^th, 2012 at 8:00am

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