[BiO BB] php and seqret

[Peter Rice]

Kim Clarke wrote:
> Hi folks,
> I'm a first year bioinformatics undergraduate nearing completion of my 
> first
> year project. A quick question...I am writing a very simple web server 
> using
> basic html and php. One section of the php deals with calling Seqret
> (EMBOSS) using exec(). Seqret is stored on the same file server and the
> command line instruction when ran in a terminal works fine. here is the
> snippet of code:
> 
>   //exec("touch $pass_c");
>   exec("seqret embl:$accession $pass_c");
> 
> both $accession and $pass_c work fine. Can anyone with experience of PHP 
> and
> EMBOSS help me? is it a problem with file permissions?

if you add "-debug" to the command line, seqret will write a file seqret.dbg in 
the current directory (wherever it runs) that will give you more clues.

My guess is that it is not finding the database definitions.

Two applications you can try are:

embossversion -full (lists all the defined paths)
showdb -full        (lists all the available databases)

if the emboss.default file or the .embossrc file for the user running the php 
are not found, you may be missing a definition for embl.

Hope that helps. Ask again if you need more clues.

Peter Rice
EMBOSS developer