Remove more remainings of qiime1

qiime(1) -- Quantitative Insights Into Microbial Ecology

This is a short 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 at http://environmentalomics.org/bio-linux-training/.

## 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

usr/lib/qiime/bin