[Bioperl-l] StandAlone BLAST on Windows???

Chris Fields cjfields at uiuc.edu
Fri Apr 21 14:23:01 EDT 2006




> -----Original Message-----
> From: Alexander Kozik [mailto:akozik at atgc.org]
> Sent: Friday, April 21, 2006 1:05 PM
> To: Bornman, Daniel M
> Cc: Chris Fields; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] StandAlone BLAST on Windows???
> 
> It looks as a query file was located on
> -i  C:\DOCUME~1\Home\LOCALS~1\Temp\QZwYdo9eKx
> "Documents and Settings" Windows directory.
> NCBI BLAST on windows does not understand white spaces in file names and
> folders/directories. Removing of white space(s) from file names and
> directories may solve the problem. Also, pay attention to the short
> style "DOCUME~1" of these names in this particular report.
> 
> Alexander Kozik
> Bioinformatics Specialist
> Genome and Biomedical Sciences Facility
> 451 East Health Sciences Drive
> University of California
> Davis, CA 95616-8816
> Phone: (530) 754-9127
> email#1: akozik at atgc.org
> email#2: akozik at gmail.com
> web: http://www.atgc.org/
> 
> 
> Bornman, Daniel M wrote:
> > All that you have asked about is in place.
> >
> >
> > 1) My PATH variable is set to 'C:\BLASTDB\bin\'
> >
> >
> > 2) the 'ncbi.ini' file is in the C:\WINDOWS directory
> > The contents of this file are:
> >
> > [NCBI]
> > Data=C:\BLASTDB\data
> >
> >
> > 3) I formatted the ecoli.nt database with the following command in the
> > DOS prompt...
> >
> > formatdb -i ecoli.nt -p F -o T
> >
> > ...this generated 7 files in the C:\BLASTDB\data\ directory.
> > (I can generate a Blast output with the following command..."blastall -p
> > blastn -d ecoli.nt -i test.txt -o test.out")
> >
> >
> >
> > 4) I also tried running the script after commenting out the
> > "$ENV{BLASTDIR} = 'C:\\BLASTDB\\data';" section
> >
> >
> >
> > BUPKIS...
> >
> >
> >
> > HAS ANYONE HERE EVER TRIED AND HAD SUCCESS USING 'StandAloneBlast' ON
> > WINDOWS?
> >

Really not the best way to go about asking for help.  I'm looking into it.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign



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