[Bioclusters] blat and hmmer on some architectures?

Jason Stajich jason.stajich at duke.edu
Tue Oct 25 08:05:25 EDT 2005

re: blat

Now that is not really fair about changing all the makefiles, you  
only need to edit inc/common.mk to set the CFLAGS/COPT and CC  
options.  I built blast with icc on i686 and gcc on x86_64 with no  

I don't understand why you think i686 is only supported.  just set  
the $MACHTYPE variable.

echo "MACHTYPE is: '$$MACHTYPE'" ; \
                 echo "it should be something simple: i386 i686 sparc  
alpha x86_64 ppc, etc..." ;

So just edit the inc/common.mk to specify your compiler flags and set  
the MACHTYPE environment variable to uname -m


On Oct 25, 2005, at 5:11 AM, Tim Cutts wrote:

> 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.
> Tim
> -- 
> 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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Jason Stajich
Duke University

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