[Biopython] Primer3Commandline rookie question

[Jukka-Pekka Verta]

OK,  the primer3 installation should be fine as I am able to run the primer3_core program from the command line with the example that comes with the distribution. I reported this to EMBOSS, let's see what they have to say...

Thank you for all the help!

JP




On 2010-11-04, at 1:53 PM, Peter wrote:

> On Thu, Nov 4, 2010 at 5:33 PM, Jukka-Pekka Verta <jp.verta at gmail.com> wrote:
>> 
>> You're right, thats the case. Still, with -oligosize changed to -osizeopt
>> Python returns me an error and running the eprimer3 on the command
>> line gives me
>> 
>>   EMBOSS An error in eprimer3.c at line 317:
>> eprimer3: Could not exec primer3_core
>> Segmentation fault
>> 
>> JP
> 
> Wow - it looks like you may have found a bug in EMBOSS itself,
> getting a "Segmentation fault" is never a good sign.
> 
> Have you properly installed the Whitehead institute primer3
> package? The EMBOSS tool acts as a wrapper, and from
> the error perhaps it can't find the primer3 tool?
> 
> You may want to report this to EMBOSS directly...
> See also: http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/eprimer3.html
> 
> Peter