Tools‎ > ‎QIIME‎ > ‎Install QIIME‎ > ‎


How to change QIIME default settings?

1) Check QIIME default settings

# start qiime
source activate qiime1

# show default QIIME settings -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"

# 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 -t
assign_taxonomy_id_to_taxonomy_fp:    /home/.../gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
                     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