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GCG and NQS

J-L. Risler risler at genetique.uvsq.fr
Wed Jan 10 13:04:16 EST 1996


In article <4cu6lr$a73 at larry.rice.edu>, fant at babs.rice.edu says...
>
>Has anyone ever configured GCG to use NQS as the batch mechanism for 
long
>sequence searches and alignments under GCG?  Unix batch is pretty much 
useless
>for any sort of serious load balancing and scheduling, and I am in the
>process of setting up NQS or some decendent thereof to handle scheduling
>on our local cluster.  I would like to use it for long GCG runs as well, 
>if anyone can make any suggestions as to how to do this.
>
>Thanks in advance,
>                Andy
>
Andy,

I run both GCG and NQS here (on a Dec2100 under DU), and there is no need 
to "configure" GCG to run in the batch mode with NQS (I agree with you 
that the Unix batch is not a batch...)

Suppose I want to run FASTA. What I do is:

- create a file named "fasta.sub" which will be some sort of:

#-----------------------------------
source /my_gcgdir/gcgstartup
gcg
/my_gcgdir/gcgbin/execute/fasta -nomon -opt -align=10 << END
my_query_seq


embl:*
6
100
my_output_file
0
END
#---------------------------------------

And then you just type "qsub fasta.sub" and here it goes....

In fact, for more interactivity and more friendliness to the others, the 
fasta.sub file is created by a simple Perl script that asks the user what 
he (she) wants.

Go for NQS. It's just great, and a REAL batch!!

Good luck,

Jean-Loup
-- 
-------------------------------
Jean-Loup RISLER
risler at genetique.uvsq.fr
Universite de Versailles
45 Avenue des Etats-Unis
78035 Versailles France
-------------------------------




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