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Perl pipeline to GCG - parameter problem

Mary Logue marylogue at hotmail.com
Wed Apr 4 07:26:44 EST 2001


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")

I still get prompted for all these parameters and although the default .msf 
file gets created, I get a message at the end saying:

sh[2]: -GAP=8: not found


Can anyone help?

Many thanks!

Mary Logue,
Bioinformatics program,
University of Ulster, Coleraine, Northern Ireland
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