FW: [Bioperl-l] LocalBlast.pm running under Apache

Barry Moore bmoore at genetics.utah.edu
Wed Dec 14 12:37:28 EST 2005

 You are exactly right.  Thanks a million, you saved me hours of
 frustration.  I'm really going to have to sit down and read that Apache
 manual sitting on my desk - or at least open it and look at the index!
 Even though this isn't a bioperl problem, I'll detail it a bit here so
 that it will hopefully Google for others searching for a similar
 While setting up a local BLAST server with a web interface using
 Bio::Tool::Run::LocalBlast and Bio::SearchIO::Writer::HTMLResultWriter
 came across the problem that the same BLAST search would work correctly
 while running as non-CGI script, but would return "***** No hits found
 ******" if running as a CGI script.  The thing that was confusing me
 that I expected BLAST to crash if it wasn't seeing both BLASTDB and
 BLASTMAT correctly.  I had explicitly set the path to the database in
 call to Bio::Tools::Run::StandAloneBlast->new which was apparently
 allowing BLAST to run, but finally noticed in the apache error logs
 apache was 'Unable to open BLOSUM62'.  This is where Marc came to the
 rescue pointing out to me that even if I had set BLASTMAT and BLASTDB
 the apache user, I would have to add the following line to
 ...so that those environment variables would be passed to the script.
 > -----Original Message-----
 > From: Marc Logghe [mailto:Marc.Logghe at DEVGEN.com]
 > Sent: Wednesday, December 14, 2005 1:05 AM
 > To: Barry Moore
 > Subject: RE: [Bioperl-l] LocalBlast.pm running under Apache
 > > -----Original Message-----
 > > From: bioperl-l-bounces at portal.open-bio.org
 > > [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of
 > > Barry Moore
 > > Sent: Wednesday, December 14, 2005 6:30 AM
 > > To: Barry Moore; bioperl-l
 > > Subject: RE: [Bioperl-l] LocalBlast.pm running under Apache
 > >
 > > Ignore this question.  There's some problem with access to
 > > BLOSUM62 even though the permissions look fine and BLASTMAT
 > > is set correctly for apache.  It's late so I'll worry about
 > > it tomorrow, but it's not a bioperl problem.
 > Hi Barry,
 > Don't know if this is the issue here or not but I think I will never
 > forget this one (cos I spent ages to find out what was going wrong):
 > even if an environmental variable is set for user apache it is not
 > automatically exported when apache is launched. You have to set
 > or pass it (PassEnv) explicitely in httpd.conf.
 > Cheers,
 > Marc

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