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