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Old 01-11-2013, 03:40 AM   #1
DimitriusSantiago
Junior Member
 
Location: Brasil

Join Date: Jan 2013
Posts: 1
Default Providing Blast Alignment (help)

Hi,
I'm working in a protein database and I need to provide Blast search tool in its webpage, but there's a problem with BLAST.cgi file (I guess): when one send the search, only appears the following text on the page:

#!/bin/csh -f

#
# $Id: blast.cgi,v 1.1 2002/08/06 19:03:51 dondosha Exp $
#

echo "Content-type: text/html"
echo ""

#setenv DEBUG_COMMAND_LINE TRUE
setenv BLASTDB db

./blast.REAL

Do someone know where's the problem ?
Thanks!
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Old 01-11-2013, 10:01 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

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Posts: 1,543
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Is CGI enabled? Is that file marked as executable?
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Old 01-11-2013, 10:31 AM   #3
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
Default

This page has instructions for setting up Web version of blast. Would not be a bad idea to verify that you have installed yours correctly. Specially the part about apache configuration.

http://blog.pansapiens.com/2008/08/2...ubuntu-apache/
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Old 01-11-2013, 10:36 AM   #4
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
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To emphasize Peter's point, your web server must be enabled to allow CGI scripts to run from the directory where the blast.cgi file is located. Some web servers allow script execution from anywhere however common practice is to put scripts in isolated directories or via the use of the cgi-wrap program.
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