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

Fields, Christopher J cjfields at illinois.edu
Tue Oct 18 14:35:08 EDT 2011


A patch is fine.  Also, it might be worth talking to the WUSTL group on merging those changes from their fork in (fairly easy to do).

At some point, if this code looks as if it needs to exist independently of bioperl-ext we can create a new repo for it.  I think it will see more use that way.

chris

On Oct 18, 2011, at 7:43 AM, jmf wrote:

> Hi
> I agree that it'd be nice to see it revived. I made a patch to the Bio/
> Ext/Align/Makefile.PL to make the compiler happy, just by changing:
> 
> 'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',
> to
> 'MYEXTLIB'  => '\'-fPIC libs/libsw$(LIB_EXT)\'',
> 
> Thanks Dave for the topic !
> 
> Chris can you correct the file or should I submit the patch (I don't
> know where ?)
> 
> On 2 sep, 17:20, Jack Tanner <i... at hotmail.com> wrote:
>> 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::Alignfor 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<cjfie... 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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