[Debian-med-packaging] r7374 - in trunk/packages/qiime: . 1.3.0_ubuntu_lucid/debian 1.3.0_ubuntu_lucid/debian/patches

[Tim Booth]

Hi Andreas,

> Just for the sake of interest: Is python2 not ported to Lucid?

I looked into it, but the python2 module for DH is in the "python"
package:

http://packages.ubuntu.com/natty/all/python/filelist

This serves as both a meta-package for Python and a collection of helper
scripts.  It auto-generates itself in exciting ways.  I wondered if I
could roll a version that incorporated dh_python2 and still played
nicely with the default version of Python on Lucid but I came unstuck.
For Qiime it just seemed easier to work from the old source package to
get a working Qiime 1.3 DEB.
 
> > Anyone wanting to package Qiime 1.3 or above for Deb Med should ignore this fork, and
> > work from the much neater trunk.  However, you should take a look at my last changelog
> > entry as there are some important changes from the packaging point of view - primarily
> > the inclusion of a small piece of compiled code
> 
> Which is what?

qiime/support_files/denoiser/FlowgramAlignment contains three Haskell source files plus a Makefile 
to handle compile/clean.

> > and the incorporation of Denoiser within
> > the core Qiime codebase.
> > ... 
> > Modified: trunk/packages/qiime/1.3.0_ubuntu_lucid/debian/changelog
> > ===================================================================
> > +Conflicts: denoiser
> > +Replaces: denoiser
> 
> 
> Is there really any need for duplicating this code instead of using the
> Debian packaged version of denoiser?

The standalone Denoiser is obsolete, with the newest version of Denoiser
being distributed within the Qiime tarball.  So I could have the qiime
source package produce a separate denoiser DEB but then looking at the
other functions of the Qiime components there is no real reason why
Denoiser should be split out anyway.  I think its existence as a
separate package is purely due to the desire of the authors to write a
separate publication for this component of the pipeline, and to
demonstrate their denoising feature in contrast to the similar feature
in the Ampliconnoise toolkit.  (Note that Qiime 1.3 is able to use the
denoising feature from Ampliconnoise if that package is installed - this
component is called Pyronoise and there was previously a standalone
Pyronoise download, but no Debian package for it as far as I know).

> BTW, I really wonder for what reason denoiser and qiime are hanging
> around in experimental.  Steffen, could you please comment on this.

The main issue as far as I know is that Qiime depends on non-free
components for standard operation.  UClust is the main offender.  For
now, on BL, we just ship the offending binary within the
"bio-linux-qiime" wrapper package.  As sequence clustering is a fairly
common task, and Qiime is a priority tool for BL, I'm confident that at
some point an alternative can be substituted and the whole lot will be
suitable for inclusion in Main.

Denoiser is free, but as per my comments above I don't think it should
be a separate package any more.

Cheers,

TIM

-- 
To Err is human.
To Arrr is Pirate!