[BioRuby] help wtih bioruby wrapper for emboss tools...

[Toshiaki Katayama]

Hi Sharvari,

What version of the BioRuby are you using?

When I tried interactively, SOAP query to EBI was successfully submitted.

------------------------------------------------------------
ktym at toge9064:~% bioruby
Loading config (/Users/ktym/.bioruby/shell/session/config) ... done
Loading object (/Users/ktym/.bioruby/shell/session/object) ... done
Loading history (/Users/ktym/.bioruby/shell/session/history) ... done

. . . B i o R u b y   i n   t h e   s h e l l . . .

  Version : BioRuby 1.2.1 / Ruby 1.8.6

bioruby> emboss = Bio::EBI::SOAP::Emboss.new
ignored attr: {}nillable
  ==> #<Bio::EBI::SOAP::Emboss:0x1978dd4 @driver=#<SOAP::RPC::Driver:#<SOAP::RPC::Proxy:http://www.ebi.ac.uk/cgi-bin/webservices/WSEmboss>>, @log=nil, @wsdl="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl">
bioruby> emboss.list_methods
  ==> ["run", "checkStatus", "getResults", "getTools", "poll", "getInfo"]
bioruby> hash = {
bioruby+ "tool" => "water",
bioruby+ "asequence" => "uniprot:alk1_human",
bioruby+ "bsequence" => "uniprot:alk1_mouse",
bioruby+ "email" => "ebisoap at example.org"
}
  ==> {"asequence"=>"uniprot:alk1_human", "tool"=>"water", "bsequence"=>"uniprot:alk1_mouse", "email"=>"ebisoap at example.org"}
bioruby> poll = emboss.run(hash, [])
  ==> "emboss-20080108-19402170"
bioruby> emboss.checkStatus(poll)
  ==> "RUNNING"
------------------------------------------------------------

Real problem here is that the EBI server never finishes this work...
5 hours later, the process is still (reported to be) running
thus I can't obtain the result yet.

------------------------------------------------------------
bioruby> emboss.checkStatus(poll)
  ==> "RUNNING"
bioruby> base = emboss.poll(poll, "tooloutput")
  ==> nil
------------------------------------------------------------

Regards,
Toshiaki Katayama


On 2008/01/09, at 4:03, Sharvari Gujja wrote:

> Hi all,
>
> I am trying to use emboss tool "water" in bioruby. However when I try to run the following script I get the error as : uninitialized constant Bio::EBI (NameError).
>
> Do I need to import any files?
>
> #!/usr/bin/env ruby
> require 'bio'
> require 'base64'
> emboss = Bio::EBI::SOAP::Emboss.new
>
> emboss.list_methods
>
> hash = {
> "tool" => "water",
> "asequence" => "uniprot:alk1_human",
> "bsequence" => "uniprot:alk1_mouse",
> "email" => "ebisoap at example.org"
> }
> poll = emboss.run(hash, [])
> emboss.checkStatus(poll)
> base = emboss.poll(poll, "tooloutput")
> puts Base64.decode64(base)
>
>
> Thanks
> -S
>
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