[Bioperl-l] Bb-utils

[Weigang Qiu]

Hi, Chris,

I just signed up for github with the username "weigangq". One of my team
member is Girish Ramrattan <gramratt at gmail.com> with the username
"gramratt3"

thanks for your facilitation,

On Mon, Dec 15, 2014 at 3:01 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

>  Weigang,
>
>  Probably will be named ‘bp-utils’, though this can be changed:
>
>  https://github.com/bioperl/bp-utils
>
>  Just to make sure, what is your Github ID (along with anyone else from
> your lab contributing to it)?  I can add a team for that repo.
>
>  chris
>
>  On Dec 15, 2014, at 1:49 PM, Weigang Qiu <weigangq at gmail.com> wrote:
>
>   Pablo, Chris, and George,
>
>  I'm glad to know that there are other similar ongoing efforts & this may
> grow into a joint project. (I agree that many commonly-used methods are
> better refactored back into API.)
>
>  Thanks for the ideas and support. It would be great if some of you could
> set up a broadly themed, developer-enticing repo ("bputils", "bioutils",
> "user-supplied utilities", "workflow tools", ?) and wiki page under bioperl
> so we could proceed to fill the content.
>
>  Thanks & best,
>
>  weigang
>
>
> On Sun, Dec 14, 2014 at 2:30 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
>
>>  It’s ‘approved' :)
>>
>>  Easy enough to set up a repo within the bioperl space for this and
>> grant permissions to whomever (just need a github account).  We just need a
>> name for the repo.
>>
>>  We can also set up a wiki presence on http://bioperl.org, but we’ve
>> been discussing (off-list) using the GitHub wiki (or readthedocs) and
>> setting up a GitHub Pages portal for projects:
>>
>>  https://help.github.com/articles/user-organization-and-project-pages/
>>
>>  This might may be a good place to start such an initiative.
>>
>>  chris
>>
>>  On Dec 13, 2014, at 11:48 PM, Weigang Qiu <weigangq at gmail.com> wrote:
>>
>>  Hi, George, Chris, and Cacau:
>>
>> That's my question as well: these are bp wrappers and utility scripts,
>> not APIs that fits into CPAN naturally. I have an informal source-forge
>> repository for bp-utils, but not quite ready for form formal release.
>>
>> My intention of having it somehow housed within bioperl is not only for
>> exposure and attracting usage and development, but also to pay proper
>> tribute to you guys' hard work maintaining and developing bioperl.
>>
>>  I appreciate the suggestion of having its own name space. If approved,
>> I (and my lab members) will make sure it doesn't not fall into poor
>> maintenance and being an orphan. Having a wiki presence may be a good first
>> step to gradually and properly roll it out?
>>
>>  thanks,
>>
>> On Sat, Dec 13, 2014 at 11:12 PM, Fields, Christopher J <
>> cjfields at illinois.edu> wrote:
>>
>>>  On Dec 13, 2014, at 3:11 PM, George Hartzell <hartzell at alerce.com>
>>> wrote:
>>>
>>> > Fields, Christopher J writes:
>>> >> Hi Weigang,
>>> >>
>>> >> I wonder whether it would be better to have a separate bputils repo
>>> >> in the BioPerl space.  This would allow development to continue w/o
>>> >> tying it directly to a release, and I think would solve the
>>> >> exposure problem much more so than having it included in the main
>>> >> bioperl-live repo.  We could also feasibly include it as part of
>>> >> the main CPAN bioperl release, maybe by simply linking to it as a
>>> >> git submodule and packaging it up.
>>> >> [...]
>>> >
>>> > Given how hard you've been working to break things out of the core and
>>> > keep orphan things that *are* in core working, I'd suggest that there
>>> > would have to be a really pressing technical reason (and longterm
>>> > support commitment) to include the the main CPAN release.
>>> >
>>> > Seems *way* cleaner to wrap it up into it's own CPAN release, give it
>>> > a good, evocative name, and make sure the distribution is well built
>>> > (correct meta info, dependencies, etc...).
>>> >
>>> > Then it'll be easy to find, easy to install and will not increase the
>>> > support burden of the core (or complicate the ongoing cleanup).
>>> >
>>> > Errr, wait.  Someone *did* ask what I thought, didn't they? :)
>>> >
>>> > g.
>>>
>>>  Yes to all of this :)
>>>
>>> My only question would be, are there a lot of distributions that consist
>>> primarily of scripts that rely completely on another distribution?
>>>
>>> chris
>>
>>
>>
>>
>> --
>> Weigang Qiu (邱伟刚)
>> 117-14 Union Turnpike
>> AC3
>> Kew Gardens, New York 11415
>> 1-917-678-3301
>>
>>
>>
>
>
> --
> Weigang Qiu (邱伟刚)
> 117-14 Union Turnpike
> AC3
> Kew Gardens, New York 11415
> 1-917-678-3301
>
>
>


-- 
Weigang Qiu (邱伟刚)
117-14 Union Turnpike
AC3
Kew Gardens, New York 11415
1-917-678-3301
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