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First things first: you should not edit or remove Qiime/qiime/support_files/qiime_config.
Some QIIME scripts read default values from a qiime_config file. The default location of this file is (Qiime/qiime/support_files/qiime_config). QIIME scripts pull default values from this file which are system-specific, such as paths to executable files, and these can be overwritten for convenience. The recommended procedure for overwriting these defaults is to copy the qiime_config file to either ~/.qiime_config or a location specified by the environment variable $QIIME_CONFIG_FP.
The Qiime configuration values should only be modified in these copies of the qiime_config file, as changes to the Qiime/qiime/support_files/qiime_config version may be overwritten in future QIIME updates.
When defaults are loaded, all three locations are checked in order of precedence. Lowest precedence is given to the Qiime/qiime/support_files/qiime_config file, as these are defaults defined by the QIIME development team and are likely not relevant to other users’ environments. Higher precedence is given to the file specified by $QIIME_CONFIG_FP, and this is envisioned to be used for defining system-wide defaults. Finally, highest precedence is given to ~/.qiime_config, so users have the ability to overwrite defaults defined elsewhere to have maximum control over their environment (e.g., if testing an experimental version of their cluster_jobs script). Note that these values are defaults: the scripts typically allow overwriting of these values via their command line interfaces.
Note that users can have up to three separate qiime_config files, and one is provided by default with QIIME. At least one qiime_config file must be present in one of the three locations, or scripts that rely on qiime_config file will raise an error. Not all values need to be defined in all qiime_config files, but all values must be defined at least once. This is one more reason why you should not edit or remove Qiime/qiime_config: when new values are added in the future they will be defined in Qiime’s default copy, but not in your local copies.
To see the qiime_config values as read by QIIME, and to test your settings, you can call:
Qiime/scripts/print_qiime_config.py -t
If you have installed QIIME using its setup.py script, you will need to set the qiime_scripts_dir value in your qiime_config file to the directory containing the QIIME scripts. By default, this will likely be /usr/local/bin/. If you specified a different location by passing --install-scripts= to setup.py, you should set qiime_scripts_dir to this value.
