[Bioperl-l] Proposal for bioperl-run

Tue Aug 26 15:57:47 UTC 2014

That's a great thought. For my next trick, I was planning ot think 
about https://github.com/bioperl/bioperl-run/issues/11 - how to deal 
with dependencies within BioPerl given the splits. I can include setting 
up travis to test in these thoughts (and perhaps actions)-- unless 
someone else is already working on this...
MAJ

On 2014-08-26 00:27, Fields, Christopher J wrote:
> \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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