Bioperl: distributing blast searches across multiple local machines

[Tim Beissbarth]

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Hi Chris!

Chris Dagdigian writes:
 > Is anyone aware of any public domain code that handles the
 > details of spreading lots of blast searches out over many
 > local machines?
I think there is a number of solutions to distribute Programs on a
cluster of Workstations. We usually use "codine" which is not free
though. But I heared there is a non comercial predesessor of codine.

 > I'm about to start writing one in perl so that I can
 > make more efficient use of our various Alpha boxes. I'm
 > not talking about anything super heavy duty-- just spreading
 > load over a small number of very high-end servers.
For personell use I wrote a very simple perl script to iterate through
a number of files the same command. I did this to run for example a
blast for each sequence file in a directory, I also added a feature to
distribute the jobs on a set of local machines. It uses rsh to
start the commands, you only need to have the same or a very similar
directoy structure on all of the machines. You get a simple help about
the basic Functions by just typing the command.


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 > If nothing is publically available, any pointers, warnings,
 > code snippets or horror stories would be appreciated.
Well maybe this helps you. Yet, I'm sure there is still a lot of bugs
in it. I am changing it whenever I notice one. I would be happy if you
would let me now of bugs or tell me major improvements or ways you
implemented things yourself. 

Cheers,

Tim

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