[Bioperl-l] Blast doesn't work

[Marc Logghe]

Hi Anders,
I use to set the blast environment explicitely in the script itself in a
BEGIN block, e.g.
BEGIN
{
    $ENV{BLASTDIR} = '/usr/local/blast/bin';
    $ENV{BLASTDATADIR} = '/home/anst/blast/data';
}

HTH,
Marc



> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of 
> Anders Stegmann
> Sent: Wednesday, December 21, 2005 4:34 PM
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Blast doesn't work
> 
> Andreas, 
>  
> Yes, I did create a file named .ncbirc and it is placed in my 
> blast working dir (/home/anst/blast/). It say's: 
> 
> [NCBI]
> Data=/home/anst/blast/data 
>  
> Anders. 
>  
>  
> 
> >>>Andreas Boehm <andreas.boehm at virchow.uni-wuerzburg.de> 
> 12/21/05 3:26 
> >>>pm >>>
> Anders,
> 
> did you create a file named .ncbirc in your working directory?
> If yes, then please post a snipped of an strace. We then can 
> have a look on what your program is trying to to.
> 
> regards,
> Andreas
> 
> 
> Anders Stegmann wrote:
> >Torsten,
> >  
> >SUSE 10.0 is the brand new version the linux SUSE OS.
> >  
> >writing: export PATH=/usr/local/blast/bin:$PATH./bptutorial 23
> >  
> >gives me:
> > 
> >bash: export 
> >PATH=/usr/local/blast/bin:/home/anst/bin:/usr/local/bin:/usr/
> bin:/usr/X
> >11R6/bin:/bin:/home/anst/blast/bin:/usr/games:/opt/gnome/bin:
> /opt/kde3/
> >bin:/usr/lib/mit/bin:/usr/lib/mit/sbin./bptutorial 23: No 
> such file or 
> >directory
> >  
> >Yes! there is definitely a file called blastall in the 
> /usr/local/blast/bin directory and it works if I use it 
> independently of bioperl.
> >  
> >The thing is that I have never before needed/used to 
> download the ncbi blast program independently.
> >Shouldn't it be enough to install the Bundle?
> >  
> >Also, when writing
> >  
> >perl -w bptutorial.pl 23
> >  
> >I get:
> >  
> >Beginning run_standaloneblast example...
> >[blastall] WARNING: Test1: Unable to open ecoli.nt.nin
> >  
> >------------- EXCEPTION  -------------
> >MSG: blastall call crashed: 256 /usr/local/blast/bin/blastall -p  
> >blastn  -d  /usr/local/blast/bin/data/ecoli.nt  -i  
> /tmp/zM1t9HD2jq  -o  
> >/tmp/FCGPZQlclD
> >  
> >STACK Bio::Tools::Run::StandAloneBlast::_runblast 
> >Bio/Tools/Run/StandAloneBlast.pm:732
> >STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast 
> >Bio/Tools/Run/StandAloneBlast.pm:680
> >STACK Bio::Tools::Run::StandAloneBlast::blastall 
> >Bio/Tools/Run/StandAloneBlast.pm:536
> >STACK main::__ANON__ bptutorial.pl:3279 STACK main::run_examples 
> >bptutorial.pl:4156 STACK toplevel bptutorial.pl:4245
> >  
> >Notice in line 2: Unable to open ecoli.nt.nin. This is a 
> remnant from an E.coli. database formatation I did much 
> earlier and independently of bioperl.
> >Thus, the ncbi standaloneblast program works, but not with bioperl!
> >  
> >Why does bioperl fetch an unrelated file in the 
> /usr/local/blast/data directory?
> >Is like it is trying to run something it shouldn't.
> >  
> >Anders.
> > >>>Torsten Seemann <torsten.seemann at infotech.monash.edu.au> 
> 12/21/05 
> > >>>12:50 pm >>> >I have tried  >export 
> BLASTDIR=/usr/local/blast/bin  
> > >>>(where my blastall binary is) >I get the same?  (I 
> assume you are 
> > >>>on Unix, not Windows)  Does it work when you do this?  export 
> > >>>PATH=/usr/local/blast/bin:$PATH ./bptutorial 23  Is there 
> > >>>definitely a file called 'blastall' in 
> /usr/local/blast/bin which 
> > >>>is EXECUTABLE and READABLE by the user running the tutorial?  -- 
> > >>>Torsten Seemann Victorian Bioinformatics Consortium, Monash 
> > >>>University, Australia http://www.vicbioinformatics.com/
> >
> >
> >
> 
> 
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