[EMBOSS] specify primer3 directory?

[Paul Tanger]

This works as well.  I didn't look at eprimer32 because for some reason I
thought the "32" was a 32 bit version or something..
Turns out eprimer32 is built to work with 2.x versions of primer3.
As Petar suggested, for a non default install of primer3 you need to modify
some files before everything will work.

To provide more detail in case others are interested, in thal_main.c you
need to modify lines 306-307:

     } else if ((stat("/opt/primer3_config", &st) == 0)  &&
S_ISDIR(st.st_mode)) {
       tmp_ret = get_thermodynamic_values("/opt/primer3_config/", &o);

and in primer3_boulder_main.c you need to modify lines 517-521:

    } else if ((stat("/opt/primer3_config", &st) == 0)  &&
S_ISDIR(st.st_mode)) {
      thermodynamic_params_path =
        (char*) malloc(strlen("/opt/primer3_config/") * sizeof(char) + 1);
      if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
      strcpy(thermodynamic_params_path, "/opt/primer3_config/");


These changes apply to unix - I saw different places in those files that
would need to be changed if you were doing this in windows.

Has anyone got emboss and eprimer32 working and installed in galaxy?  Or a
similar primer design tool in galaxy?

Thanks for the help everyone.


Message: 6
Date: Fri, 14 Sep 2012 11:06:47 +0300
From: Petar Petrov <ppetrov at mail.student.oulu.fi>
Subject: Re: [EMBOSS] specify primer3 directory?
To: emboss at lists.open-bio.org
Message-ID: <20120914110647.sacof6lkgscookc0 at webmail.oulu.fi>
Content-Type: text/plain; charset=windows-1251; DelSp="Yes";
        format="flowed"

Hi Paul,

which version of primer3 do you use? What operating system? How did
you install primer3 and EMBOSS?

If it is primer3 version 2.* I think you should use eprimer32 wrapper
instead and it expects primer3_core to be called primer32_core. To
make primer3 aware of another location of the primer3_config
directory: it seems that two files need to be modified before
compiling: thal_main.c and primer3_boulder_main.c (in the subfolder
src).

Hope this helps.

regards,

Petar