[Bioperl-l] Proposal for bioperl-run

[Mark A. Jensen]

All,
Can people have a look at bioperl/bioperl-run branch 
topic/move_WrapperBase 
(https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase) and 
see what they think. I used filter-branch to generate a (local clone of) 
bioperl-live containing only Bio/Tools/Run and t/tools, then merged this 
into a topic/move_WrapperBase branch of bioperl-run. If this looks ok, 
give me the signal and I will merge into master. Next step would be to 
remove these items from bioperl-live.

thanks MAJ


On 2014-08-22 12:59, Fields, Christopher J wrote:
> On Aug 22, 2014, at 10:50 AM, Francisco J. Ossandón
> <fossandonc at hotmail.com> wrote:
>
>> 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??
>
> No updates to 1.6.x if they have been moved out (with the exception
> of Bio::Root).
>
> We need to end-of-life 1.6.x at some point.  It's worth having a
> meeting to talk about what needs to be done and to maybe discuss
> 1.7.x(Google or IRC).  IRC may be easier.I can set up a poll, maybe
> see who wants to participate...
>
>> 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.
>
> WrapperBase is essentially the common core for all the wrappers (a
> few don’t use it, but most do).  So it really belongs in bioperl-run,
> as well as StandAloneBlast.  The only real reason this and the other
> Tool::Run modules were in bioperl-live was legacy, but I think this
> hampers bioperl-run development frankly, as it relies on bioperl-live
> (via WrapperBase).  If all the wrapper code were part of bioperl-run
> fixes would be much easier to make and release independently.
>
>> 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??
>
> Yes, go ahead and do that.
>
> -c
>
>> 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
>>
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