[Bioperl-l] Bb-utils

[Weigang Qiu]

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
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