[Bioperl-l] EMBOSS tools and bioperl

Orvis, Joshua D. (HSC) Joshua-Orvis at ouhsc.edu
Thu Aug 5 12:25:39 EDT 2004

my "needle" is in /usr/local/bin, and if that isn't in apache's path you could do something like this at the top of your CGI script:

$ENV{'PATH'} = "/usr/local/bin";


$ENV{'PATH'} .= ":/usr/local/bin";  ## if you want to keep the existing PATH as well


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org on behalf of SRMD, Col - Underwood, Anthony
Sent: Thu 2004-08-05 11:05 AM
To: bioperl-l at bioperl.org
Cc: SRMD, Col - Chandra, Manosree
Subject: [Bioperl-l] EMBOSS tools and bioperl
Hi bioperlers

I have a perl program using bioperl and the EMBOSS factory module.

The program works fine from the command line but not as cgi which is
obviously running as a different user.

I have a suspicion it's something to do with paths. Is there an
environmental variable I need to set to run emboss programs as there is with
local blast and bioperl e.g 
BEGIN {$ENV{BLASTDIR} = '/usr/local/blast';$ENV{BLASTDATADIR} =
'/usr/local/blast/data/databases';  }

When I run these two lines within the script

$factory = Bio::Factory::EMBOSS -> new();
$needle = $factory->program('needle') || die "needle_factory $!";
<----------line 23

the error message is 
needle_factory No such file or directory at
/usr/local/apache/cgi-bin/needle_test.cgi line 23.
Please can anybody advise.

Many thanks


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