[bip] Reproducible research

[Giovanni Marco Dall'Olio]

On Wed, Mar 4, 2009 at 6:01 PM, Bruce Southey <bsouthey at gmail.com> wrote:
>> Just using a script is far less useful than a make style system.  If
>> the first step on the script is, say, to download and formatdb a large
>> database you only want to run these once if possible.  Yet you want
>> them to be in the script because they are necessary first steps.
>>
> That is complete rubbish because the makefile is just a script!
> Further, I do not see how a makefile would be useful here. Sure you can
> tell it run formatdb if the database has 'changed' but it is not easy
> check if it should download a database.

The biomake link posted before is very interesting. Unfortunately, it
is not clear whether the project is alive or not.

Look at this presentation:
- http://skam.sourceforge.net/biomake-bosc-presentation.pdf  (it's a pdf)

I like the syntax which seems clear and they way it creates a blast
database only if it is really needed.


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