[Biopython-dev] Biopython AlignAce Wrapper

[Christian Brueffer]

(CC'ing biopython-dev)

Thanks for the feedback.

I'd propose the following plan for the AlignAce wrapper then:

1. Submit the cleanup patches I have to give the wrapper at least a
    fighting chance at actually working
2. Add a BiopythonDeprecationWarning
3. Remove the wrapper after 1.61 is released (except the situation
    changes of course)

Does that sound acceptable?

Chris


On 12/17/2012 05:25 PM, Bartek Wilczynski wrote:
> Well,
>
> sounds like a good plan. I think the situation is hopeless: If we had
> the source of AlignAce with appropriate license we could think of
> supporting it ourselves, but in this situation I guess we can only
> deprecate the module and phase it out...
>
> best
> Bartek
>
> On Mon, Dec 17, 2012 at 10:10 AM, Christian Brueffer
> <christian at brueffer.de> wrote:
>> Hi Bartek,
>>
>> thanks for checking.  The thing is, the "new" version is actually an
>> ancient version:
>>
>> AlignACE version 2.3  October 27, 1998
>>
>> I made it work by installing Fedora Code 3 in a VM and using
>> elfstatifier to bind AlignAce and all libraries into one executable.
>> I works, but I doubt it's of any use these days.
>>
>> I wonder whether it's better to remove the wrapper.  The AlignAce
>> developers are unresponsive, none of the Biopython people has a
>> version and from what I can see the current wrapper cannot possibly
>> work.
>>
>> What do you think?
>>
>> Chris
>>
>>
>> On 12/17/2012 05:01 PM, Bartek Wilczynski wrote:
>>>
>>> Hi,
>>>
>>> I've looked around and it seems I don't have it. We probably need to
>>> "update" the parser to work with the current version of AlignACE
>>> available from Harvard. Were you able to run it? On mys system, it
>>> cannot find the libraries it needs...
>>>
>>> best
>>> Bartek
>>>
>>> On Fri, Dec 14, 2012 at 7:05 AM, Christian Brueffer
>>> <christian at brueffer.de> wrote:
>>>>
>>>> Hi Bartek,
>>>>
>>>> I currently clean up the Biopython AlignAce wrapper.  Unfortunately
>>>> I've been unable to obtain the latest AlignAce version since the
>>>> download page disappeared and the Church lab is unresponsive.
>>>>
>>>> Do you happen to have a version of AlignAce 4.0 for Linux lying around,
>>>> that you could send me?
>>>>
>>>> Thanks a lot,
>>>>
>>>> Chris
>>>