[Bioclusters] re: how to run mpiblast

[Glen Otero]

On Jul 16, 2004, at 6:22 PM, kenix y wrote:

> mpiBLAST is ready to run in BioBrew.
>
> 1)I had set up .ncbirc
>
> [NCBI]
> Data=/opt/BioBrew/NCBI/6.1.0/data
> [BLAST]
> BLASTDB=/tmp/blast
>
> 2) and mpiblast.conf
>
> /mnt/pvfs
> /tmp/blast
> /opt/BioBrew/NCBI/6.1.0/bin
>
> 3) edit my /etc/profile
> export BLASTPATH=/opt/BioBrew/NCBI/6.1.0/bin
> export MPIBLASTCONFIG=/home/bigcpuguest/mpiblast.conf
> export MPIRUN=/usr/bin/mpirun
>
> 4) my $HOME/machines contains
> comp-pvfs-0-0
>
> Can anyone tell me what is the correct command if I want to run 
> mpiblast against ecoli.nt?

We have to know what directory you keep the input file and the db in on 
the frontend, but here is the general idea:

$MPIRUN -np <number of procs> -machinefile $ 
/path/to/file/with/nodelist $BLASTPATH/mpiblast 
--config-file=$MPIBLASTCONFIG -p blastn -i /path/to/query -d 
/path/to/ecoli.nt -o /path/to/results_file
>
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Glen Otero, Ph.D.
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