[Bioclusters] re: how to run mpiblast

Glen Otero bioclusters@bioinformatics.org
Wed, 14 Jul 2004 23:46:27 -0700

On Jul 14, 2004, at 11:28 PM, kenix y wrote:

>> You will need to create one where you run mpiblast, and in your home 
>> directory.
> Meaning that I need to create .ncbirc in /root, is that right?

There's a problem with running things out of the /root directory, as 
Joe mentioned, because that directory isn't NFS mounted over the whole 
cluster in BioBrew. You need to get into a user directory under /home 
to make mpiBLAST work.
> [NCBI]
> Data=../data
> BLASTDB=../db
> Er, I'm not too sure where the weight matrices are, any way I can find 
> out?

The matrices are here:

So an .ncbirc file that looks like this:

will do the trick.
>> Then edit the BLASTDB=../db line to point to the database (ecoli.nt 
>> in your case).
> As for ecoli.nt, I've just moved it to /tmp/blast
> So the line should be
> BLASTDB=/tmp/blast/ecoli.nt?


>> You will need a copy of this in you home directory and in the 
>> directory you run the mpiblast code.
> As for the directory to run my mpiblast code, it can be anywhere? Or 
> is there a specific location?

I typically run mpiBLAST from my home directory, after creating the 
mpiblast.conf file there. Here's an mpiblast.conf example:

[glen@frontend-0 glen]$ more mpiblast.conf

This dictates that all the input data files for mpiBLAST are stored in 
/home/glen/data, they will be stored in /tmp on the compute nodes, and 
that the mpiBLAST binary lives in /opt/BioBrew/NCBI/6.1.0/bin (with the 
rest of the blastall binaries).


> Thanks for all your help
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Glen Otero, Ph.D.
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