Wrappers for ExaML, ExaBayes, *BEAST

[rvosa]

Hi,

not sure if this is the right place to ask but we have been writing some Bio::Tools::Run::Phylo::* wrappers (for the above-mentioned programs) that we would like to contribute to bioperl-run. The code that we have now is here: https://github.com/naturalis/supersmart/tree/master/lib/Bio/Tools/Run/Phylo

What would we need to do to make them so that they are acceptable to bioperl-run? We introduced a dependency that you probably don't want (though we only use it for data munging that we can probably do some other way), and there's the complicating issue that these tools want to be run under MPI so the wrappers have getters/setters for mpirun, and the command string is a longer. Other than that we've tried to be faithful to the Bio::Tools::Run::Phylo API.

Thanks!

@hettling & @rvosa

[majensen]

I can look at this, Rutger Cheers MAJ

On Mon, May 04, 2015 at 7:56 AM, Rutger Vos < [email protected] [[email protected]] > wrote: Hi,

not sure if this is the right place to ask but we have been writing some Bio::Tools::Run::Phylo::* wrappers (for the above-mentioned programs) that we would like to contribute to bioperl-run. The code that we have now is here: https://github.com/naturalis/supersmart/tree/master/lib/Bio/Tools/Run/Phylo [https://github.com/naturalis/supersmart/tree/master/lib/Bio/Tools/Run/Phylo]

What would we need to do to make them so that they are acceptable to bioperl-run? We introduced a dependency that you probably don't want (though we only use it for data munging that we can probably do some other way), and there's the complicating issue that these tools want to be run under MPI so the wrappers have getters/setters for mpirun, and the command string is a longer. Other than that we've tried to be faithful to the Bio::Tools::Run::Phylo API.

Thanks!

@hettling [https://github.com/hettling] & @rvosa [https://github.com/rvosa]

— Reply to this email directly or view it on GitHub [https://github.com/bioperl/bioperl-run/issues/14] .[https://github.com/notifications/beacon/AAFAmbXuc4fAGvpbZgoABugjlc9mJoRVks5oF1YVgaJpZM4EPQ9P.gif]

[rvosa]

Thanks, let me know what we need to do to get these wrappers into a nice home :) Cheers, Rutger