INVOCATION:

To run any QIIME command such as "validate_mapping_file.py":

$ qiime validate_mapping_file [...]

or just type 'qiime' to get a customised 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.

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.

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.

PROGRAMS INVOKED BY QIIME:

QIIME calls many applications and libraries in the course of performing an analysis. For consistency, it is important to know what versions were installed at the time of the analysis. To obtain a complete report type

print_qiime_config_all

NB: The official release of QIIME stipulates very particular versions of all these programs in order to guarantee consistent results. This version of QIIME uses updated versions that are packages in the Debian software repository. If you want to obtain ressults consistent with the official QIIME pipeline then you need to install QIIME as set out on the main website.

UCLUST and USEARCH:

You may install these manually if you want to use them, but as of QIIME 1.9 all features should be available via the free SumaClust and vSearch programs. uClust and uSearch 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

QIIME was packaged as part of the Bio-Linux project.

http://environmentalomics.org/bio-linux