[GSoC] Possible project

[Peter Cock]

Licence wise you can bundle any or all of Biopython.
Breaking it up might be rather fiddly through.

There are Python installation approaches for an
all-in-one tool release of a tool - best bet may
depend on your target platform. I think Tiago does
something like this for his population genetics tools
where his libraries are in Biopython... could we
discuss this on the Biopython mailing list?

Petr

On Wednesday, February 26, 2014, Rob Lanfear <rob.lanfear at gmail.com> wrote:

> That's a great idea.
>
> Is it possible to include functions from BioPython directly into the
> program?
>
> I would love to use the SeqIO modules and a few other things, but I
> haven't done so to date because I need the program to be batteries
> included. I would lose almost all of my users if I started asking them to
> install Python dependencies.
>
> Cheers,
>
> Rob
>
>
> On 27 February 2014 08:11, Hilmar Lapp <hlapp at drycafe.net<javascript:_e(%7B%7D,'cvml','hlapp at drycafe.net');>
> > wrote:
>
>> Perhaps such integration could even be the GSoC project idea.
>>
>>    -hilmar
>>
>>
>> On Wed, Feb 26, 2014 at 1:33 PM, Brad Chapman <chapmanb at 50mail.com<javascript:_e(%7B%7D,'cvml','chapmanb at 50mail.com');>
>> > wrote:
>>
>>>
>>> Peter and all;
>>> Seconding Pjotr's comments, I think it would be a good challenge to try
>>> and be more inclusive in projects we can work with. This is a good
>>> chance to have OpenBio get more mentors and contributors. Conversely,
>>> this
>>> is an opportunity for projects like Rob's to try and integrate better
>>> with the OpenBio community and code. As a practical example, from quickly
>>> scanning the source it looks like PartitionFinder has PhyML and RaXML
>>> integration code that could benefit from using Biopython's support for
>>> these tools, contributing back things that Biopython is missing.
>>>
>>> Peter, would adding contributions and Biopython integration along these
>>> lines satisfy your concerns? Rob, would Biopython integration be
>>> something you have interest in tackling along with your other goals for
>>> the summer?
>>>
>>> Brad
>>>
>>>
>>> > On Wed, Feb 26, 2014 at 7:29 AM, Rob Lanfear <rob.lanfear at gmail.com<javascript:_e(%7B%7D,'cvml','rob.lanfear at gmail.com');>>
>>> wrote:
>>> >> Hi All,
>>> >>
>>> >> To clarify, I'm not a NESCent organiser, just a mentor who was hoping
>>> to
>>> >> put a specific project through NESCent. The link is for the project,
>>> whose
>>> >> title is "Automated partitioning for morphological phylogenetics":
>>> >>
>>> >>
>>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2014#Automated_partitioning_for_morphological_phylogenetics
>>> >>
>>> >> It's a Python (and some external C programs) project, which does not
>>> use
>>> >> any of the Bio* projects. So the questions are really specific to
>>> that one
>>> >> project - I'm interested to know if this is the kind of thing that OBF
>>> >> might consider as a project.
>>> >>
>>> >> Cheers,
>>> >>
>>> >> Rob
>>> >
>>> > Given it doesn't use or extend any of the OBF's Bio* projects,
>>> > as it stands, I don't see this as a obviously a good fit :(
>>> >
>>> > Perhaps there's a possible slant on this I've overlooked?
>>> >
>>> > Regards,
>>> >
>>> > Peter
>>> > (OBF secretary, Biopython developer, etc)
>>> > _______________________________________________
>>> > GSoC mailing list
>>> > GSoC at lists.open-bio.org<javascript:_e(%7B%7D,'cvml','GSoC at lists.open-bio.org');>
>>> > http://lists.open-bio.org/mailman/listinfo/gsoc
>>> _______________________________________________
>>> GSoC mailing list
>>> GSoC at lists.open-bio.org<javascript:_e(%7B%7D,'cvml','GSoC at lists.open-bio.org');>
>>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>>
>>
>>
>>
>> --
>> Hilmar Lapp -:- lappland.io
>>
>>
>
>
> --
> Rob Lanfear
> Research Fellow,
> Ecology, Evolution, and Genetics,
> Research School of Biology,
> Australian National University
>
> phone: +61 (0)2 6125 3611
>
> www.robertlanfear.com
>
>