[Bioclusters] blat and hmmer on some architectures?

Tim Cutts tjrc at sanger.ac.uk
Tue Oct 25 05:11:02 EDT 2005

On 24 Oct 2005, at 7:44 pm, Vsevolod (Simon) Ilyushchenko wrote:

> Hi,
> Our lab is starting to test several server architectures by  
> compiling and timing programs like blast, blat and hmmer. The  
> setups are Darwin, regular i686, Intel's and AMD's X86_64 and IBM's  
> ppc64.
> I've found that blat only has the i686 machine type as a  
> compilation option - not x86_64, and of course not Darwin or ppc64.  
> Hmmer is smarter better - it only lacks support for ppc64 (it has  
> plain ppc though). Does anyone know if it's possible to compile  
> blat and hmmer on these architectures?

I don't see why not, as long as you're using a suitable compiler.   
You'll just need to work out what the appropriate compiler options  
are.  HMMER will probably work fine on ppc64, since it already  
supports other 64-bit architectures fine.  The same goes for BLAT -  
it works fine on Alpha for us, so I see no reason why it shouldn't  
compile OK on other 64-bit architectures.

You'll have fun finding the bazillion places in Jim Kent's makefiles  
that you need to make the changes though.


Dr Tim Cutts
Informatics Systems Group, Wellcome Trust Sanger Institute
GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5  860B 3CDD 3F56 E313 4233

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