IUBio

Anyone using standalone Primer3?

Todd Scheetz todd-scheetz at uiowa.edu
Fri Jun 4 10:29:41 EST 1999


Jil,

You have tried re-directing STDIN, right? We use Primer3 here as a
stand-alone package, and I've included an example of what a command
looks like when we run it. (with the executable named primer.)

% primer <  selected.1998-03 > candidates.1998-03

So selected.1998-03 is the input file in Boulder IO format, and the
candidates.1998-03 file is the outputfile.

Hope this helps,
-Todd



Jil Tardiff wrote:
> 
> What a week!  I will not devulge the ugly details, but suffice it to
> say, I have to get a standalone Linux workstation up and running with
> some basic molbio packages.
> 
> Almost everything is going OK at present (big thanks to Alan Williams),
> but I am very stumped with Primer3.
> 
> This machine is *not* hooked up to the Internet, so we need to use a
> standalone primer prediction package.
> 
> The machine is running RH 6.0 (I'm not sure what version of gcc to be
> honest) and kernel 2.2.9 .
> 
> First of all, I cannot get the source packages to pass the
> primer_test.pl file, it bombs almost immediately. (the executable
> *seems* to compile OK).  So, I tried a statically linked ELF binary, but
> (and this is the embarrassing part), I cannot figure out *what* the
> exact command line should be!  I have an example file in Boulder IO
> format and the program kicks out "Format should be ./primer3
> [-format_output] " and that it takes standard input.  I've tried
> multiple permutations to no avail.
> 
> This is frustrating in the extreme (to say the least), and data is
> piling up on me....(and my poor student)
> 
> Any and all help would be greatly appreciated,
> 
> Jil




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