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

[Albert Vilella]

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
>
>