Anyone using standalone Primer3?

Jil Tardiff jtardiff at westnet.com
Sat Jun 5 08:55:55 EST 1999


Todd,

You hit the nail on the head.  I've been learning UNIX/Linux from the ground
up and for the life of me I couldn't figure out how to redirect STDIN!  Really
basic.  And strangely enough, none of the several books I checked explained
explicitly how to do it.

Oh well, live and learn.  The standalone Primer3 seems quite nice. My student
is *thrilled*. She designed her last set of human-based primers by hand. She
did a great job, but it was painful, so I think this will help her out.

Thanks again,

Jil





Todd Scheetz wrote:

> 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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