Use two Emboss package with one database

[David Martin]

On 21/5/03 9:59 am, "Peter Rice" <pmr at ebi.ac.uk> wrote:

> yann-francois.bizouerne at bayercropscience.com wrote:
>> Hello,
>> 
>> I am working with 2 diffretns servers on different locations. On each of them
>> a
>> EMBOSS package tools is installed.
>> I need to know if I could configure these 2 EMBOSS in order to work with the
>> same database (which is located on one of the two servers).
>> Is EMBOSS could working this way or does I need to have only one EMBOSS
>> package
>> (tools + databse) installed on one server ?
> 
> Yes ... but you need to do some work.
> 
> The EMBOSS package on the same server as the databases is easy.
> 
> The second EMBOSS package needs to read from remote databases. I assume
> you indexed them with dbiflat (an the other dbi programs).
> 
> You can access a remote database by:
> 
> SRSWWW if it on an SRS server
> URL if you have a web page to query the database
> APP (EXTERNAL) if yuo have a script that can return an entry
> 
> Assuming you don't have them under SRS ...
> 
> You can provide a simple web CGI script that runs entret (for whole
> entry) or seqret (for sequence only - you can put -osformat on the
> command line to get the format of your choice))
> 
> You can write a script that will access the databases somehow (possibly
> also by talking to a web page - your choice).
> 
> Meanwhile, I am working on ways to define EMBOSS web services and data
> services that would give an alternative access method, but that is for
> later in the year.
> 

What about just using Jemboss (or a variant thereof) to talk to the master
machine? The alternative is shunting lots of data around which isn't really
feasible unless you have a fast network between the machines.

Do you move the data to the problem or the problem to the data? The trade
off is between transport time and execution time.

Does Jemboss make use of a SOAP server? If not it would be really nice to
have a script that could generate a WSDL definition from the ACD files.

It's then one step away from being a Grid service..

..d 

 
 

-- 
David Martin PhD
Bioinformatics Scientific Officer
Post-Genomics and Molecular Interactions Centre
University of Dundee