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,