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:
print_qiime_config.py -t
Setting qiime_scripts_dir¶
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.
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 filter_alignment.py
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 assign_taxonomy.py (and parallel versions)
assign_taxonomy_id_to_taxonomy_fp
: default id-to-taxonomy map to use with assign_taxonomy.py (and parallel versions)
sc_queue
: default queue to submit jobs to when running parallel QIIME on StarCluster