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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 that are available:

$ module avail qiime2

Load a particular version into your environment and run it:

$ module load qiime2/2018.6
$ qiime --help

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
$ conda update -n base conda
$ wget https://data.qiime2.org/distro/core/qiime2-2018.6-py35-linux-conda.yml
$ conda env create -p /export/apps/qiime2/2018.6 --file qiime2-2018.6-py35-linux-conda.yml
$ conda activate /export/apps/qiime2/2018.6
$ 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). My strategy is to install Conda somewhere globally and then use it to install Qiime2. After the installation is done I think we don't technically need Conda itself anymore, but but I will keep it around for ease of upgrading and installing future versions.

To create the modulefile I compared the output env before and after loading the Qiime2 environment with Conda.

qiime2-software.txt · Last modified: 2018/07/22 19:21 by aorth