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This is a proto-manpage for Qiime on Debian/Bio-Linux.
Some of this info alternatively belongs in README.Debian.
INVOCATION:
To run a Qiime command such as check_id_map.py:
% qiime check_id_map [...]
or just type 'qiime' to get a shell environment where all Qiime commands are available, ie:
% qiime
% qiime > check_id_map.py [...]
PARAMETERS FILE:
For certain qiime commands, you need to indicate where your qiime parameters file is. You
should make a copy of the default version at /usr/share/doc/qiime/qiime_parameters.txt and
edit it to suit your needs. A key thing to edit is the location of your greengenes
database and lanemask files.
You either need to have your edited copy of your qiime parameter file in your working
directory, or you need to give the path to the file using the -p parameter in the relevant
qiime commands.
GREENGENES DATA:
Make sure that you have copies of the greengenes core set data file (fasta) and the
greengenes alignment lanemask file installed. These do NOT come with the bio-linux-qiime
package. You must edit your custom parameter file in your working directory to give the
full path to these files.
QIIME CONFIGURATION:
Qiime reads configuration information from the file specified by QIIME_CONFIG_FP.
Your QIIME_CONFIG_FP is set to /etc/qiime/qiime_config. It is unlikely you will need to
change the settings in this file.
UCLUST:
You may need to install UClust manually to use some Qiime functions.
For more info, try running 'uclust' at the qiime prompt.
For more information about Qiime, please refer to the Qiime documentation at:
http://qiime.sourceforge.net/
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