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Perl pipeline to GCG - parameter problem

Simon Andrews simon.andrews at bbsrc.ac.uk
Thu Apr 5 02:55:36 EST 2001


Mary Logue wrote:
> 
> Hello!
> 
> I'm trying to create a perl pipeline to GCG, but when I type:
> 
> system("pileup \"@\"test.list -GAP=8 -LENgth=2 -DENsity=20.0
> -OUTfile=test.msf")

On our system this works;

system ('/path/to/pileup @file.list -gap=8 -len=2 -out=test.msf -def');

You may not need to include the full path to pileup in your command if
it's in your default path (ours isn't).

If you need to have variable interpolation in the command then you could
also write this as;

my $filename="file.list";
system ("/path/to/pileup \@$filename -gap=8 -len=2 -out=test.msf -def");


Hope this helps

Simon.


PS On a technical note, this isn't actually a pipe to pileup (which is
also possible), but rather just an external command call - which was
what it sounded like you were actually trying to do.




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