[Bioclusters] Condor cluster and BLAST

[Paul]

Great response for Sandy. I am in a similar position with a new cluster 
in our lab. I am still very early in the learning curve and your 
comments for Sandy are very helpful. We have and all vs all Blast job 
that we would like to run. I am trying to get a handle on how best to 
run this. I am wondering if you have any comments regarding all vs all 
tools. I am aware of blastn but was considering maybe Blat instead. We 
are mainly interested in high homology hits and the increased speed of 
Blat might be of value. Do you have any experience with Blat? If so how 
difficult do you think it would be to use it in an all vs all setup. Any 
comments would be great. I am a bit over my head at the moment. Thanks
We have rocks 4.1 installed along with the biobrew roll. Currently we 
have about 14 cpus.

Paul Mc Kenna



Christopher Dwan wrote:

> Sandy,
>
> First the nitty gritty:
> --------------------------
> * I recommend using the binary downloads at ftp://ftp.ncbi.nih.gov/ 
> blast/. If computation is ever the limiting factor on your system then 
> switch over to custom binaries.
>
(snip)