[BioPython] biopython integration with make-like tools (e.g. waf, paver)

[Peter]

>> That sounds potentially useful for a complicated analysis pipeline.
>> But suppose you also wanted to check the current version of BLAST
>> installed and the version of BLAST used in the existing output file?
>> This would probably be possible within a Makefile using some embedded
>> shell scripts calling grep, but it wouldn't be very nice at all.
>> Although it would still be a non-trivial bit of code, I would prefer
>> to do this in python (maybe put the code into a library function for
>> reuse).
>
> well, in principle you would check for blast's executable last
> modification date.
> If the blast executable has a modification date which is younger than
> the results file, you will have to calculate them again.

That might work, but is a slightly different check.  Just because the
executable is "newer" doesn't mean its a different version.

> Other build tools can also check for md5 modification to prerequisite
> files, or can be integrated with subversion/other rcs systems.
> You can do this in python, but it takes a lot of time, and would mean
> re-writing existing code. I am sure there is should be something
> specific for bioinformaticians already :).

There might be, but I don't see this kind of thing as specific to
bioinformatics.  Data analysis pipelines could be applied to any
scientific data analysis, e.g. meteorological data analysis.

> Well, I'll write some workflows with the tools I linked before (and
> also with scons) and let you know.

I guess the best way to evaluate the tools is to try using them :)

Good luck,

Peter