[Bioperl-l] blastall call --- cannot find index files for databases

[Liu Haifeng]

Sorry, it still doest not work.  Actually, theres is no problem when I use
"blastall -p blastn" to query nucleotide sequences in my bio-perl script.

Regards
Haifeng
----- Original Message -----
From: "Jason Stajich" <jason@cgt.mc.duke.edu>
To: "Liu Haifeng" <lhaifeng@dso.org.sg>
Cc: <bioperl-l@bioperl.org>
Sent: Friday, May 03, 2002 8:20 PM
Subject: Re: [Bioperl-l] blastall call --- cannot find index files for
databases


> On Fri, 3 May 2002, Liu Haifeng wrote:
>
> > Hi,
> >
> > I just met another problem.  I have used "formatdb -o T ..." to
> > construct one protein database "mydbname" whose defline is like
> > "gnl|sth|sthelse".  It is ok if I directly perform blastall query in
> > my linux console window.  Howvever, if I perform a perl script which
> > uses Bio::Tools::Run::StandAloneBLast to call blastall, then the
> > program always crashes and shows "WARNING: Could not find index files
> > for database mydbname ...".  I have set $BLASTDATADIR in my .bashrc
> > file.
>
> You've just identified the problem - when blast is shelled out it uses
> 'sh' and the env variable is only set in your bash shell, it is not
> propigated to th sh process.
>
> options:
> when you specify the db use the full path to the db i.e. in your perl
> script you could use the shortcut that you know your
> BLASTDATADIR contains the db
> $factory->d($ENV{'BLASTDATADIR'}.'/databasename');
>
> Put the env variable in your .profile or .login (at least I *think* this
> might work).
>
> >
> > Could anyone help me to solve the problem?
> >
> > Regards
> > Haifeng
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Haifeng Liu
> > Ph.D., Member of Technical Staff
> >
> > IFL/DS
> > DSO National Laboratories
> > 20 Science Park Drive
> > Singapore 118230
> >
> > Email: lhaifeng@dso.org.sg
> > Tel: (65) 67728220
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>