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QIIME2

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. QIIME2 is a completely new and different version than QIIME1.

Information

Usage

See versions of qiime2 which are available:

$ module avail qiime2

Load a particular version:

$ module load qiime2/2018.4

Installation

Notes from the sysadmin during installation:

$ 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. I install Conda somewhere globally so that I can use it to install Qiime2. After the installation is done you don't technically need Conda itself, but Qiime2 will need Conda's Python so we must keep it around. I compared the output env before and after loading the Qiime2 environment with Conda, then used that to create the module file.

qiime2-software.txt · Last modified: 2018/05/21 10:01 by aorth