QIIME™ (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.

• Version: 2018.4
• Added: May, 2018
• Link: https://qiime2.org/

See versions of qiime2 which are available:

$ module avail qiime2

Load a particular version:

$ module load qiime2/2018.4

Notes from the sysadmin during installation. Install Conda somewhere globally, but not used by anyone, then use that Conda to install Qiime2:

$ cd /tmp
$ sudo mkdir /export/apps/qiime2
$ sudo chown aorth:aorth /export/apps/qiime2
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh -p /export/apps/qiime2/conda
$ source /export/apps/qiime2/conda/bin/activate
$ wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-linux-conda.yml
$ conda env create -p /export/apps/qiime2/2018.4 --file qiime2-2018.4-py35-linux-conda.yml
$ conda activate /export/apps/qiime2/2018.4
$ sudo chown -R root:root /export/apps/qiime2
$ qiime --help

Qiime2 has 240 dependencies and is extremely tricky to install without the use of Miniconda—it is not even published on PyPy anymore, so installing it with pip is not an option.