Re: Where is Bio-Graphics?

On 2/20/17, 9:27 AM, "[email protected] on behalf of Carnë Draug" <[email protected] on behalf of [email protected]> wrote:



>On 20 February 2017 at 01:03, Fields, Christopher J
><[email protected]> wrote:
>> On 2/19/17, 3:51 PM, Carnë Draug <[email protected]> wrote:
>>
>>>On 19 February 2017 at 21:25, Brian Osborne <[email protected]> wrote:
>>>>> On Feb 19, 2017, at 3:17 PM, Carnë Draug <[email protected]> wrote:
>>>>>
>>>>> I came across Bio-Graphics [1] which was once part of the BioPerl
>>>>> distribution.  However, I can't find it in any of the bioperl repos.
>>>>> Could anyone point me to it?
>>>>>
>>>>> Carnë
>>>>>
>>>>> [1] https://metacpan.org/release/Bio-Graphics
>>>>
>>>> https://github.com/GMOD/Bio-Graphics
>>>>
>>>
>>>So is Bio-Graphics part of the GMOD project and not BioPerl?
>>
>> Lincoln could probably best indicate the history here, but
>> Bio-Graphics was actually part of the main bioperl distribution for
>> quite a while (up until 1.5.2 I think).  IIRC we felt it best to
>> split it out around the time that Gbrowse2 development kicked into
>> high gear, since it’s a pretty self-contained set of modules with a
>> sometimes troublesome-to-install dependency (GD).  We left it up to
>> Lincoln, who I think felt it best fit under the GMOD umbrella.
>>
>
>The way I came across Bio-Graphics was through bioperl-live logs.
>This seems to have been the first distribution to be excised from the
>core in 2009 [1] but also seems to have been an independent event and
>not part of the plan to reorganise bioperl into smaller modules which
>only appears mentioned in 2011 [2].
>
>The pod of Bio-Graphics still only mentions the bioperl project in the
>feedback section so that's a bit confusing.  It reads like it's part
>of bioperl.  A link on their metadata file to the repository or bug
>tracker could also help.
>
>Carnë
>
>[1] https://github.com/bioperl/bioperl-live/blob/master/Changes#L714
>[2] https://github.com/bioperl/bioperl-live/blob/master/Changes#L375

Correct; much of the incentive I believe was the need to push out a new Bio::Graphics release, which was hindered by the lack of bioperl releases at that time.  This worked, and also suggested that further splitting out of code would likely work.  

My suggestion would be (depending on your time) adding a Github issue and possibly generating a pull request with the specific changes.  I have commit for Bio-Graphics I think, so I should be able to merge that in

chris




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