[Bioclusters] blat and hmmer on some architectures?

Joe Landman landman at scalableinformatics.com
Tue Oct 25 07:27:49 EDT 2005

Hi Simon:

   I had rebuilt the HMMer for ppc from source for MacOSX 64bit a number 
of months ago.  It was fairly simple as I remember, using the rather 
common methods for autoconf based software:

	./configure --prefix=/path/to/where/you/want/to/install/it
	make test
	make install

   You can pull down the binary 32 bit versions from Sean Eddy's site. 
It does work pretty well (as a 32 or 64 bit application).  BLAT should 
be also simple to compile, though as Tim indicated, as it should be a 
simple matter of Makefile edits.

   FWIW: we have a nice fast build of HMMer (no source changes) 
available for x86_64.  About 40ish% faster than the gcc based HMMer on 
the same machine for our test cases in BBS.  Contact me offline if you 
would like to use it for testing.


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?
> Thanks,
> Simon

Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
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