[Bioperl-l] Proposal for bioperl-run

[Francisco J. Ossandón]

I have also looked 

I don't mind the moving of those modules but I would like to ask something. Any future updates to the moved modules should also be added, if possible, to the modules that will remain v1.6.x branch? Or their development would be freezed?? Or should they also be removed from there too??

I've been keeping the synchronicity of updated modules that were moved out of -live into their own repo with their versions in v1.6.x branch (like Root and Coordinate), but the synch of WrapperBase when mixed into other existing repo like Run will depend on if it start to depend on code of other Run modules or not.

On a side note, I just realized that there is an empty "hmmer3.pm" file in "bioperl-live/Bio/Tools/Run"... It seems to have been added already empty in https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, maybe by mistake. It appears to be the only empty file in the repo. Should I delete it??

Cheers,

Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org [mailto:bioperl-l-bounces+fossandonc=hotmail.com at mailman.open-bio.org] En nombre de Mark A. Jensen
Enviado el: viernes, 22 de agosto de 2014 8:09
Para: Fields, Christopher J
CC: George Hartzell; bioperl-l at mailman.open-bio.org
Asunto: Re: [Bioperl-l] Proposal for bioperl-run

Thanks Chris-- yes, you must be right. I just did a quick grep for "StandAloneBlast" in the modules. I will verify and leave bl2seq alone.
Will do everything in branches and then give the signal- cheers MAJ On 2014-08-21 23:50, Fields, Christopher J wrote:
> On Aug 21, 2014, at 9:37 PM, George Hartzell <hartzell at alerce.com>
> wrote:
>
>> Mark A. Jensen writes:
>>> [...]
>>> My simple proposal is to move these three modules from bioperl-live 
>>> to bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, 
>>> btw).
>>>
>>> Thoughts?
>>> [...]
>>
>> Speaking from a safe distance, that sounds *wonderful*.
>>
>> g.
>
> Agreed.  Also, I think you mean that StandAloneBlast has a dependency 
> on AlignIO::bl2seq, not the other way around, correct? At least, I 
> didn’t see anything there.
>
> If no one objects to it (give it a day), I say go ahead and move it 
> over.
>
> chris

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