[Bioperl-l] Proposal for bioperl-run

Tue Aug 26 04:27:55 UTC 2014

\o/

Not sure but we should probably set up Travis-CI tests for bioperl-run; lots of apps available via apt.

-c

On Aug 25, 2014, at 9:46 PM, Mark A. Jensen <maj at fortinbras.us> wrote:

> WrapperBase and friends removed from bioperl-live; Travis built successfully at #486.
> MAJ
> On 2014-08-25 22:08, Mark A. Jensen wrote:
>> Hearing no objections, I've merged topic/move_WrapperBase with
>> master. I will proceed to remove WrapperBase and friends from
>> bioperl-live.
>> MAJ
>> On 2014-08-23 15:29, Mark A. Jensen wrote:
>>> 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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>>>>> 
>>>> 
>>>> 
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