QIIME for Debian - source
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.py endings and the qiime wrapper of Bio-Linux
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Previous comment by Steffen:

Lintian complains a lot about script-with-language-extension,
i.e. the .py endings for files ending up in /usr/bin.
What to do about this is not clear for the moment. For the
time speaking it seems like lintian is wrong here, too deeply
embedded is python in the project and Debian does not
want to become incompatible.

New comments by Tim:

I borrowed the Bio-Linux approach for QIIME which may or may not be the best idea.
Essentially, the Python scripts are not in the path and instead of running:

% my_qiime_app.py

You run:

% qiime my_qiime_app.py

or equivalently just:

% qiime my_qiime_app

The 'qiime' wrapper script adds the extension if needed and sets the path.  If run with
no arguments it sets the path and drops to an interactive shell.

The dependencies of QIIME essentially make it non-free despite the DFSG licence on the QIIME
code itself.  Chief among these is UClust.  This package is supposed to handle the lack of UClust
gracefully but it is still up to the user to fetch and install it.  

Other dependencies/TODO:
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Everything else needed should be packaged, if not in Debian proper then in the SVN.  QIIME
keeps adding new deps so these need to be checked with each release.

denoiser - no longer a dependency as it has been folded into Qiime itself.
several recommended deps should probably be hard depends, as long as they are available in the archive

emperor and king are both troublesome in their own ways.  We really need Emperor for 1.8.0+

QIIME data
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The QIIME installation instructions say that you need to download some core files from Greengenes.
Since these barely change and are included in the upstream tarball I am now putting them into the
qiime-data package for easy access.  I have noted in copyright that these are CC licensed.

See here for a discussion of what these are and why they don't change:

https://groups.google.com/forum/?hl=en-US#!searchin/qiime-forum/greengenes/qiime-forum/SvXFetaLNCM/HE6bsBY0yZIJ

