[Bioperl-l] BLASTDATADIR, Standaloneblast, and CGI script

[Todd Richmond]

Thanks Jason,

That did the trick.


On 7/21/01 4:49 AM, "Jason Stajich" <jason@chg.mc.duke.edu> wrote:

> Todd - try putting your stmt in a BEGIN block for your cgi-script.
> 
> BEGIN {
> $ENV{BLASTDATADIR} = 'yadda-yadda';
> }
> 

> I'm curious how performance is with this?  We're gearing up to add more
> explict links to the ncbitoolkit in bioperl with the help from Jonathan
> Epstein, and that may or may not improve performance for you as well.
> 

Performance varies - 3 or 4 seconds to retrieve an EST sequence from a
remote MySQL database, blast it against a small local protein database, and
present the results in the browser. Much longer for a BAC sequence (85
seconds). I'm doing it primarily to remove the need to keep thousands of
static Blast reports laying around. Performance is likely to increase once I
move it to my production server - I've noticed that Blast 2.1.3 runs ~3-4
times slower under MacOS X than it does under Linux 2.2. It's probably a
compiler issue, but not one that I have the knowledge to figure out.


-- 
Todd Richmond                    http://cellwall.stanford.edu/todd
Carnegie Institution             email: todd@andrew2.stanford.edu
Department of Plant Biology      fax: 1-650-325-6857
260 Panama Street                phone: 1-650-325-1521 x431
Stanford, CA 94305