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

[Albert Vilella]

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.
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>