This is a proto-manpage for QIIME on Debian/Bio-Linux.
You should refer to the main QIIME documentation at
/usr/share/doc/qiime/html/index.html and also the QIIME section of the
Bio-Linux tutorial.

INVOCATION:

    To run any QIIME command such as validate_mapping_file.py:

	$ qiime validate_mapping_file [...]

    or just type 'qiime' to get a shell environment where all QIIME commands
    are available exactly as documented, ie:

	$ qiime
	$ qiime > validate_mapping_file.py [...]

PARAMETERS FILE:

    For certain QIIME commands, you are asked to indicate where your QIIME
    parameters file is. You can find an example file in the location
    /usr/share/doc/qiime/qiime_parameters_example.txt but the recommendation
    as of QIIME 1.7.0 is to only set values that you want to override and to
    let QIIME pick defaults for the others.

GREENGENES DATA:

    The qiime-data package now provides copies of the Greengenes core alignment
    template plus the lanemask file in /usr/share/qiime/data but you still need
    to download some extra data to use QIIME properly.  Taxonomic databases are
    being updated all the time and you need to be sure which version you are
    using.  See the QIIME main docs for more info on what you need.

QIIME CONFIGURATION:

    QIIME reads configuration information from the file specified by
    $QIIME_CONFIG_FP or by default from /etc/qiime/qiime_config. 
    It is unlikely you will need to change the settings in this file,
    but if you do you should copy it as .qiime_config in your home directory.

UCLUST and USEARCH:

    You may need to install these manually to use some QIIME functions.
    These applications are not free software and come with usage restrictions
    for non-paying users.
    For more info, try running 'uclust' or 'usearch' at the QIIME prompt.

For more information about QIIME, please visit the home page at:

    http://qiime.org
