Remote getz from emboss

Rodrigo Lopez rls at
Fri Nov 1 09:47:17 UTC 2002


(not directly related to rsh...) :-)

The EBI's External Services group is working on a web service that uses SOAP
and Axis to address this. We have a prototype running in-house that permits
us to use the service within EMBOSS as an external method. Sharmila Pilai,
who has been working on this can provide more details. From the user point
of view things look like this:

% seqret wsembl:hscfos\* -auto -out myfile.tfa

The above will use the web service to retrieve data from a source such as
SRS, server w/ cdrom index files (another emboss installation), etc. The
user needs to install a perl or java client on his/her machine an have some
bits and bobs to run the SOAP/Axis client part of the service.

Another thing we are working on is being able to use EMBOSS remotely using
the same technology, for example from a Windows2000 machine using the
command prompt. All that would be required is again a perl/java client and
general usage looks as follows:

C:\My Documents\wsemboss {appname} {params}

Obviously, all can be hidden behind batch scripts to make it even simple to
use and in effect, design a simple workflow such as:

C:\My Documents\wseqret wsembl:hscfos\* -auto -stdout |
wnewcpgreport -filter -auto

Anyway, I think Sharmila will have some more comments to make about this and
tell you more about her progress.

Sharmila, I think you should join this list (if you are not already there?).


> -----Original Message-----
> From: owner-emboss-dev at
> [mailto:owner-emboss-dev at]On Behalf Of Claude Bonnard
> Sent: 01 November 2002 09:21
> To: EMBOSS Dev
> Subject: Remote getz from emboss
> Dear,
> Does someone use a script (shell or perl) to access a srs server
> on an other
> machine with rsh? If yes, is it possible to have this script?
> the idea is to replace the "local" getz by a rgetz.
> I am aware of the gbwget development, but I am sure that the
> equivalent for
> getz has been done somewhere.
> -Many thanks in advance,
> regards,
> Claude
> --
> Claude Bonnard Ph.D.
> ISREC (Swiss Institute for Experimental Cancer Research)
> Bioinformatics Group
> Ch des Boveresses 155
> CH-1066 Epalinges
> Switzerland
> phone: [41-21]-692-5891
>   fax: [41-21]-652-6933

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