[EMBOSS] external and app

[Alexis Torrano Martinez]

Hello

I am trying to execute hmmsearch from EMBOSS. This way I want to have
a kind of wrap over the DDBB and retrieval apps. 

 
 DB Pfam [
 	method: "app"
 	comment: "Pfam with HMMER indexing"
 	app: "$HMMERBIN/hmmsearch $EMBOSS_DATA/pfam/Pfam_ls %s"
 	]

That is my DB specification for EMBOSS. How should I run seqret 
to execute properly hmmsearch? 

 seqret Pfam:$HOME/soft/hmmer/last/tutorial/7LES_DROME


And the next error was unexpected :

Error: Unable to read sequence
'Pfam:/usr/usuaris/it/inb/soft/hmmer/last/tutorial/7LES_DROME'

As tutorial says, if you specify external, %s receives as value the
second field of the query (ID from seqret DB:ID).

There is a way to call hmmsearch from EMBOSS?

           A lot of thanks.

         Regards.

    Alexis Torrano.     




--
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Alexis Torrano Martinez

Instituto Nacional de Bioinformatica (INB) Nodo
Computacional GNHC-2
UPC-CIRI
c/. Jordi Girona 1-3
Modul C6-E201           Tel.   : 934 011 650
E-08034 Barcelona       Fax    : 934 017 014
Catalunya (Spain)       e-mail : atorrano at lsi.upc.edu
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