[Bioperl-l] EMBOSS tools and bioperl

SRMD, Col - Underwood, Anthony Anthony.Underwood at hpa.org.uk
Thu Aug 5 12:31:19 EDT 2004


Thank you Joshua that was the trick- the apache user didn't have anything
defined for the $PATH variable. Specifying /usr/local/bin in a statement
like 
 
BEGIN {$ENV{PATH}='/usr/local/bin/';} at the beginning of the script did he
trick.
 
Thanks for your quick reply,
 
Anthony

-----Original Message-----
From: Orvis, Joshua D. (HSC) [mailto:Joshua-Orvis at ouhsc.edu]
Sent: 05 August 2004 17:26
To: SRMD, Col - Underwood, Anthony; bioperl-l at bioperl.org
Cc: SRMD, Col - Chandra, Manosree
Subject: RE: [Bioperl-l] EMBOSS tools and bioperl



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";

or

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

Joshua


-----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


Anthony

-----------------------------------------
**************************************************************************
The information contained in the EMail and any attachments is confidential
and intended solely and for the attention and use of the named addressee(s).
It may not be disclosed to any other person without the express authority of
the HPA, or the intended recipient, or both. If you are not the intended
recipient, you must not disclose, copy, distribute or retain this message or
any part of it. This footnote also confirms that this EMail has been swept
for computer viruses, but please re-sweep any attachments before opening or
saving. HTTP://www.HPA.org.uk <HTTP://www.HPA.org.uk>
**************************************************************************

_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l
<http://portal.open-bio.org/mailman/listinfo/bioperl-l> 






-----------------------------------------
**************************************************************************
The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************


More information about the Bioperl-l mailing list