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Running binnary program in a loop

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# 1  
Old 02-12-2011
Running binnary program in a loop
I am using a very simple script (MUS) to process some files where the input file for the binary application I am running has to be named infile. So I have this:
Code:
#!/bin/bash
for i in {1..n}
do
    mv block${i} infile
done
./dnadist <<EOF
D
Y
EOF

However, I want to use dnadist inside the loop, something like this:
Code:
#!/bin/bash
#!/bin/bash
for i in {1..n}
do
    mv block${i} infile
    ./dnadist <<EOF
    D
    Y
    EOF
done

But, of course is wrong and I only get this error:
Quote:
./MUS: line 17: warning: here-document at line 5 delimited by end-of-file (wanted `EOF')
./MUS: line 18: syntax error: unexpected end of file
I will be very thankful if some one can point me in the right direction.
Thanks!
# 2  
Old 02-12-2011
Hi
Try this:

Code:
#!/bin/bash
#!/bin/bash
for i in {1..n}
do
    mv block${i} infile
    ./dnadist <<EOF
D
Y
EOF
done

I just removed the alignment.

Guru.
# 3  
Old 02-12-2011

Put the closing EOF at the beginning of the line, or, if it is preceded by a tab, add - before the first EOF:
Code:
	./dnadist <<-EOF
	D
	Y
	EOF

# 4  
Old 02-12-2011
Great!
Please bear with me! If I do the following, would that work?

Code:
#!/bin/bash
for i in {1..2}
do
    mv block${i} infile
    ./dnadist <<EOF
D
Y
EOF
    rm infile
    mv outfile infile${1}
done

OR
Code:
#!/bin/bash
for i in {1..2}
do
    mv block${i} infile
    ./dnadist <<-EOF
    D
    Y
    EOF
    rm infile
    mv outfile infile${1}
done

Thanks!
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