[Bioperl-l] Bio::Ext::Align?

Jack Tanner ihok at hotmail.com
Fri Sep 2 11:20:44 EDT 2011


I also see that someone's forked it on Github and made some packaging fixes.

It'd be nice to see it revived.

On 9/2/2011 9:00 AM, Fields, Christopher J wrote:
> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/
>
> chris
>
> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:
>
>> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
>> http://toolkit.tuebingen.mpg.de/hhpred
>>
>>
>> He got it working thus:
>> Hi Dave,
>> thanks a lot. i made it work. The error i got later on was:
>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
>> recompile with -fPIC
>>
>> the solution is:
>> perl Makefile.PL PREFIX=<path to installation>  /fftwsingle --enable-shared --with-pic --enable-single
>> <edit Makefile to add -fPIC to CFLAGS>
>> make
>> make install
>> http://forums.fedoraforum.org/showthread.php?t=232607
>>
>>
>>
>> Dave
>>
>>
>>
>>
>>
>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J<cjfields at illinois.edu>  wrote:
>> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
>>
>> chris
>>
>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>>
>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
>>>
>>> Does anyone have a spec file for building an SRPM for it for RHEL 6?
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>>
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>
>
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