[EMBOSS] Database access external app

[Stefanie Lager]

Marc,

I use the same setup as you "app: "fastacmd -d hs_pub_genomic -s %s",
and I try to retrive from a human genome database (each chr is a BIG
fasta file). The formatdb indexing seems OK, fastacmd works on
commandline. But I don't get any error from EMBOSS it just can't retrive
entries (it just hangs there forever). 

Stefanie

> Hi Stefanie,
> Can you show the actual entry in your emboss.default file, or eventual
> error messages when running the emboss command ? We use exactly the
> same system for the worm chromosomal sequences for instance. Every
> chromosome is a separate blastable 'database'. worm_chromosomes.nal
> makes them look like 1 big. The entry looks like this: DB
> worm_chromosomes [ type: N format: ncbi
> method: app
> app: "fastacmd -d worm_chromosomes -s %s"
> ]
> 
> HTH,
> Marc
> 
>> -----Original Message-----
>> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
>> Sent: vrijdag 13 februari 2004 8:55
>> To: emboss at embnet.org
>> Subject: [EMBOSS] Database access external app
>> 
>> 
>> Hi,
>> 
>> I'm trying to retrieve entries in EMBOSS using fastacmd as an
>> external application. It works nice as long as the database, indexed
>> with formatdb, is a singe fasta file. But when I have big
>> databases that are
>> split up in volumes and use a .nal file with the names of the
>> idividual
>> files it doesn't work with EMBOSS anymore. Does anyone have
>> experience with fastacmd and EMBOSS database indexing in combination
>> with databases
>> split into volumes?
>> 
>> Stefanie
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