[EMBOSS] external and app

[Guy Bottu]

On Fri, Jun 03, 2005 at 11:15:10AM +0200, Alexis Torrano Martinez wrote:
> 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"
>  	]

	Dear Alexis,

Your problem is as good as certain that the program defined as "app" 
should return a sequence to standard output, so that EMBOSS can take it. 
And this is not what hmmsearch does. Furthermore, hmmsearch searches a HMM 
against a databank of sequences ; you seem to want to search a sequence 
against a databank of HMM's (Pfam_ls), for which you need hmmpfam. It is 
maybe a good idea to install the Embassadir HMMER. Note however that 
ehmmpfam needs the user to specify where the databank is. At the BEN site 
I have a little bit "hacked" the program so that it uses Pfam_ls by 
default (and still lets the user choose an alternative). If you are 
interested I can send you a mail with "how to".

	Guy Bottu,
	Belgian EMBnet Node