[EMBOSS] Applications limits

[Peter Rice]

Achille Zappa wrote:
> Hi All !
> I'm new in the mailing list and I want to say hello to everyones
> I want to use some EMBOSS apps as services in a Taverna workflow, but
> they failed in some cases, I suppose when I use "too many" sequences or
> alignments as inputs!! Could you tell me if there are some specific limits
> and what they are?! Especially about "emma", "fproml" and "fneighbor"
> services !

The applications are limited only by the resources of the machines they run 
on. The applications you mention are not pure EMBOSS applications. Emma is 
a wrapper for clustalw. fproml and fneighbor are from PHYLIP 3.6. They may 
have their own limits but they are large.

When using Taverna and the SoapLab services you may reach a timeout limit 
on the services. I see Mahmut Uludag has already replied on the taverna 
mailing list with a fix for that.

SoapLab services for Taverna use machines with large enough resources for 
most jobs.

If you find an example where you have reached a limit, please send it to 
emboss-bug at emboss.open-bio.org

It may be simply a large input or a long calculation - but we can try to 
improve the application to make it faster or to use less memory.

regards,

Peter Rice