soaplab-users

Re: [Soaplab-users] SOAPLab2 - EBI

[Guillaume C. <gco...@gm...>]

Dear all,

I'm looking to interface primer3 in webservice, but when you launch the
program, this one generates some files...how can I catch this results? How
can I choose a directory to generate these files, because they are generated
in tha catalina home...

Best reagards,
GC.

Re: [Soaplab-users] SOAPLab2 - EBI

[Mahmut U. <ul...@eb...>]

Hi Guillaume,

> I'm looking to interface primer3 in webservice, but when you launch
> the program, this one generates some files...how can I catch this
> results?

>  How can I choose a directory to generate these files, because they
> are generated in tha catalina home...

Did you mean, in directory "${catalina.base}/temp/_R_" ? this is the
default working directory Soaplab uses if users didn't configure their
Soaplab installation by a customised soaplab.properties file.

Relevant Soaplab properties 'working.dir' and 'results.dir' are
explained in Soaplab Configuration Guide.

http://soaplab.sourceforge.net/soaplab2/ConfigurationGuide.html#properties

Soaplab creates a new folder for each job under the 'working.dir'
directory and all job outputs should normally be under that folder.
Collection of these outputs should normally be done by defining
appropriate output types as described in Soaplab Metadata Guide.

http://soaplab.sourceforge.net/soaplab2/MetadataGuide.html#outfiles

EMBOSS has a wrapper for primer3 called eprimer3? You may find it useful
to check how EMBOSS calls eprimer3. I copied below a link to EBI
eprimer3 web service based on Soaplab.

http://www.ebi.ac.uk/soaplab/typed/services/nucleic_primers.eprimer3?wsdl

Regards,
Mahmut