[Bioperl-l] Blastall problems

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Thu Mar 29 19:50:20 EDT 2007


Simon,

> I am having a few difficulties with standaloneblast. I am trying to implement
> web tool which will blast a given sequence before it goes on to do various
> other things. I have a script to run the blast using the appropriate bioperl
> modules which runs ok from the command line. The problem comes when I > try to run this through the web page. I get this output:
> I'm not sure exactly what this means!
> Any ideas would be gratefully received.

Try putting this BEGIN{} block at the top of your Perl script:

BEGIN {
  $ENV{BLASTDIR} = '/usr/bin/';  # where my blastall binary is
  $ENV{BLASTDATADIR} = '/fs/storage/data/db/blast/' ; # where my -d are
}

This is because the CGI script doesn't necessarily get the same
environment as your login account.

Are your CGI scripts running as user apache/httpd or are you using
suEXEC to run it as 'williams' (or other) user?

--Torsten


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