Where is Bio-Graphics?

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Where is Bio-Graphics?

Carnë Draug-2
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

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Re: Where is Bio-Graphics?

Brian Osborne-2
https://github.com/GMOD/Bio-Graphics

On Feb 19, 2017, at 3:17 PM, Carnë Draug <[hidden email]> 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

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Re: Where is Bio-Graphics?

Carnë Draug-2
On 19 February 2017 at 21:25, Brian Osborne <[hidden email]> wrote:

>> On Feb 19, 2017, at 3:17 PM, Carnë Draug <[hidden email]> 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?

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Re: Where is Bio-Graphics?

Fields, Christopher J
On 2/19/17, 3:51 PM, "Bioperl-l on behalf of Carnë Draug" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:



>On 19 February 2017 at 21:25, Brian Osborne <[hidden email]> wrote:
>>> On Feb 19, 2017, at 3:17 PM, Carnë Draug <[hidden email]> 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.

chris
>

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Re: Where is Bio-Graphics?

Carnë Draug-2
On 20 February 2017 at 01:03, Fields, Christopher J
<[hidden email]> wrote:

> On 2/19/17, 3:51 PM, Carnë Draug <[hidden email]> wrote:
>
>>On 19 February 2017 at 21:25, Brian Osborne <[hidden email]> wrote:
>>>> On Feb 19, 2017, at 3:17 PM, Carnë Draug <[hidden email]> 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

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Re: Where is Bio-Graphics?

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



>On 20 February 2017 at 01:03, Fields, Christopher J
><[hidden email]> wrote:
>> On 2/19/17, 3:51 PM, Carnë Draug <[hidden email]> wrote:
>>
>>>On 19 February 2017 at 21:25, Brian Osborne <[hidden email]> wrote:
>>>>> On Feb 19, 2017, at 3:17 PM, Carnë Draug <[hidden email]> 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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Re: Where is Bio-Graphics?

Carnë Draug-2
On 20 February 2017 at 15:40, Fields, Christopher J
<[hidden email]> wrote:

> On 2/20/17, 9:27 AM, Carnë Draug" <[hidden email]> wrote:
>>
>>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.
>>
>
> 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

Done.  Please pull and compare master branch from
[hidden email]:carandraug/Bio-Graphics.git

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