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
