[Bioclusters] re: how to run mpiblast

[Glen Otero]

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
> [BLAST]
> BLASTDB=../db
>
> Er, I'm not too sure where the weight matrices are, any way I can find 
> out?

The matrices are here:
/opt/BioBrew/NCBI/6.1.0/data

So an .ncbirc file that looks like this:
[NCBI]
Data=/opt/BioBrew/NCBI/6.1.0/data

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
> [BLAST]
> BLASTDB=/tmp/blast/ecoli.nt?

Yep.

>> 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
/home/glen/data
/tmp
/opt/BioBrew/NCBI/6.1.0/bin

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).

Glen

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