Quick Start
===========

Type 'qiime' at the shell prompt before running any of the standard
qiime commands.

QIIME for Debian and Ubuntu
===========================

QIIME is a very powerful environment, but the core of its power stems
from the tools underneath.

Not all those tools that QIIME can work with are yet available with
Debian. If you find resources to help - please do.

Most of the needed tools are available via the Bio-Linux project:
http://nebc.nerc.ac.uk/tools/bio-linux . This package was one of the
first to profit from now joint forces on getting the packages to a
best-possible shape for everyone.

The package is in experimental since:
 * it depends on python-pynast that is in experimental - and since like
   pynast it uses the sphinx documentation system that it not yet uses
   to streamline the orig.tar.gz and recreate the documentation from
   its sources.  When adding python-sphinx the build fails because of
   a conflict to orig.tar.gz that could not yet be resolved.
 * qiime still lacks a man page

The distribution is set to contrib because of
 * the strong recommends to use uclust that is not shipped with
   Debian as a binary only package with a restrictive license.


Disambiguation of versions in bio-linux, Debian and Ubuntu
----------------------------------------------------------

The conflict reports in the control file is originally indicated against
bio-linux-qiime (<= bl1.1.x). The prefix "bl" is unfortunate since the
Debian packaging tools demand (and the Debian policy) demand the version
to start with a number, not a character. The version is now removed from
that indicated conflict.

Depending on who was performing the last editing of the package, versions
are either specified with a suffix "-N", N numeric, for uploads to Debian,
or with the suffix "-ubuntuN". The changelog shall show the Ns to increase
and be reset for new upstream versions. This is yet slightly different
from the common practice to have the Ubuntu version keep the last Debian
version (or start a new one as 0) and have the version extended to
"NubuntuM" with M reset to 1 with every new Debian version. Either way
makes sense. The current approach indicates better that some upload
to Debian may not yet have happened.
