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qiime_config


How to change QIIME default settings?



1) Check QIIME default settings

# start qiime
source activate qiime1

# show default QIIME settings
print_qiime_config.py -t



2) Search original qiime_config file and copy to home directory

# search location of the qiime_config file
find ${HOME} -type f -name "qiime_config"
/home/username/miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime/support_files/qiime_config

# copy file into home directory as .qiime_config (dot prefix for hidden file)
cp /home/username/path/to/original/file/qiime_config ${HOME}/.qiime_config


Change QIIME tmp directory

# Edit file .qiime_config (in home directory), open in pure text editor (not word)
nano .qiime_config

  # add new folder to temp_dir line (tab separated):
 temp_dir    /my/new/tmp/directory/


# check if new settings are working
print_qiime_config.py -t
...
assign_taxonomy_id_to_taxonomy_fp:    /home/.../gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
                         temp_dir:   
/my/new/tmp/directory/
                     slurm_memory:    None
                      slurm_queue:    None
...



# to work with all Python scripts, new tmp path needs set in shell variable TMPDIR (add export command to your .bashrc file)
export TMPDIR=/my/new/tmp/directory