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Setting up your qiime_config file

First things first: you should not edit or remove Qiime/qiime/support_files/qiime_config. Modifying or removing this file may cause QIIME to fail.

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 $HOME/.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/support_files/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.

Viewing and testing your qiime_config settings

To see the qiime_config values as read by QIIME, and to test your settings, you can call: -t

Setting qiime_scripts_dir

If you have installed QIIME using its 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, you should set qiime_scripts_dir to this value.

Definition of values in qiime_config

cluster_jobs_fp : path to your cluster jobs file. This file is described in Using parallel QIIME.

python_exe_fp : path to python executable

working_dir : a directory where work should be performed when running in parallel. You must be able to write to this directory. May be deprecated in favor of temp_dir in QIIME 1.8.0.

blastmat_dir : directory where BLAST substitution matrices are stored

blastall_fp : path to blastall executable

pynast_template_alignment_fp : default template alignment to use with PyNAST as a fasta file

pynast_template_alignment_blastdb : default template alignment to use with PyNAST as a pre-formatted BLAST database

template_alignment_lanemask_fp : default alignment lanemask to use with

jobs_to_start : default number of jobs to start when running QIIME in parallel. don’t make this more than the available cores/processors on your system

seconds_to_sleep : number of seconds to wait when checking whether parallel jobs have completed

qiime_scripts_dir : directory where QIIME scripts can be found

temp_dir : directory for storing temporary files created by QIIME scripts. when a script completes successfully, any temporary files that it created are cleaned up (if you notice this isn’t the case for some script, please let us know)

denoiser_min_per_core : minimum number of flowgrams to denoise per core in parallel denoiser runs

cloud_environment : used only by the n3phele system. you should not need to modify this value

topiaryexplorer_project_dir : directory where TopiaryExplorer is installed

torque_queue : default queue to submit jobs to when using parallel QIIME with torque

assign_taxonomy_reference_seqs_fp : default reference database to use with (and parallel versions)

assign_taxonomy_id_to_taxonomy_fp : default id-to-taxonomy map to use with (and parallel versions)

sc_queue : default queue to submit jobs to when running parallel QIIME on StarCluster