[EMBOSS] question EMBOSS-GUI

[Stefanie Lager]

SRS is set up for the user that runs EMBOSS on command line, while SRS
is NOT set up for the user (nobody) that runs through the web
interface. If you have SRS running as web interface you can use 

method: srswww
url: "http://the.adress.to local.SRS.com"

Or write a script that calls getz, and sets up SRS and use the script
with 

method: app
app: "path/to/the/script " 


Stefanie
> 
> 
> 
> 
> Hello,
> 
> I don't know if you could help me with the little problem I have.
> 
> I have installed your EMBOSS-GUI application on our server a few
> month ago. And it works great.
> Since I have installed SRS on our servern. I have mofified the
> emboss.default in order to use to the SRS indexes.
> Now it looks like :
> 
> DB TREMBL [
> methodquery: srs
> format: SWISS
> type: P
> comment: "TREMBL (SPTREMBL + TREMBLNEW) using SRS"
> app: getz
> dbalias: TREMBL
> methodall: direct
> file: "trembl.dat"
> dir: $emboss_data_dir/swall
> ]                                                                 
>                                                                   
>  
> 
> 
> And that works quitr well on command line, when I need to retrieve
> a sequence with seqret for example. But if I am using the
> EMBOSS-GUI interface I just obtain the following errror message:
> 
> EMBOSS An error in ajfile.c at line 145: execvp ('getz -e
> '[TREMBL-id:Q977L9]'', NULL) failed: 'No such file or directory'
> Error: Unable to read sequence 'TREMBL-id:Q977L9' Died: seqret
> terminated: Bad value for '-sequence' with -auto defined seqret
> exited with status 1...
> 
> Do you have a clue for the problem ?
> 
> Thanks in advance
> 
> Best regards.
> 
> 
> 
> 
> 
> 
> 
> Yann-François BIZOUERNE
> BioInformatic Team
> BAYER CropScience
> 1, rue Pierre Fontaine
> 91058 Evry Cedex
> FRANCE
> Phone:      33-(0) 1-69-47-61-56
> FAX:        33-(0) 1-69-47-61-42
> E-mail:     yann-francois.bizouerne at bayercropscience.com
> Intranet: http://bioinfo.evry.fr.bayercropscience/

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