[Bioperl-l] New Bio::Tools::Run::Phylo::SLR - Wrapper around the SLR program

[Jason Stajich]

My own icc compiled version seemed to have caused the problem.  
whoops. fixed that.
-jason
On Dec 4, 2007, at 12:39 PM, Albert Vilella wrote:

> oh, I forgot to mention: SLR uses the lapack and blas libraries if
> installed, which makes it a lot faster (according to the author)...
> maybe that's the reason...
>
> On Dec 4, 2007 8:34 PM, Albert Vilella <avilella at gmail.com> wrote:
>> hmmm, 30 minutes is quite a lot... it takes much less for me:
>>
>> avilella at magneto:~/bioperl/vanilla/bioperl-run$ time perl t/SLR.t
>> 1..7
>> ok 1 - use Bio::Root::IO;
>> ok 2 - use Bio::Tools::Run::Phylo::SLR;
>> ok 3 - use Bio::AlignIO;
>> ok 4 - use Bio::TreeIO;
>> ok 5
>> ok 6
>> ok 7
>>
>> real    0m21.517s
>> user    0m20.717s
>> sys     0m0.100s
>>
>>
>>
>> On Dec 4, 2007 5:16 PM, Jason Stajich <jason at bioperl.org> wrote:
>>> Excellent - thanks for this !  I'm giving it whirl on linux and the
>>> SLR.t test is currently taking more than 30 minutes to run -- is it
>>> possible to cook up an example that is going to finish in a more
>>> reasonable amount of time?
>>>
>>> Also - I would prefer if the default exe could be 'Slr' rather than
>>> Slr_Linux_static - it seems like it is possible for users to install
>>> it this way.  Similarly whether or not the Slr_osx or Slr is the
>>> default name, is it too big of a deal to expect the user to  
>>> rename it?
>>>
>>> I'll give it a whirl on OSX later, but might be easier if the test
>>> runs shorter.
>>>
>>> Thanks!
>>> -jason
>>>
>>> On Dec 4, 2007, at 3:51 AM, Albert Vilella wrote:
>>>
>>>> Hi all,
>>>>
>>>> There is a new wrapper in bioperl-run for SLR:
>>>>
>>>> http://www.bioperl.org/wiki/SLR
>>>>
>>>> Right now, output parsing is very simple, and I have only tested  
>>>> it on
>>>> my linux machine.
>>>> Can someone with a Mac give it a try?
>>>>
>>>> update your bioperl-run to cvs head, then:
>>>>
>>>> # try the installer, SLR is option 6
>>>> perl scripts/bioperl_application_installer.PLS
>>>> # then try to run the tests (should take about a minute)
>>>> perl t/SLR.t
>>>>
>>>> Any comments on the code would be appreciated,
>>>>
>>>> Thanks in advance,
>>>>
>>>> Cheers,
>>>>
>>>>     Albert.
>>>> _______________________________________________
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>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>