Linux

Introduction

The Linux installation of QIIME is similar to the Anaconda (Basic) steps found in the macOS section. But due to the curation of Linux packages on Anaconda Cloud, you can have the Complete installation of QIIME and perform both pre-processing steps and analysis steps on one package.

Step 1. Download and Install Anaconda

Step 1a: Update packages and install basic dependencies

# Update
sudo apt-get update

# Install basic packages
sudo apt-get install build-essential python-dev python-pip wget git

Step 1b: Download the correct Anaconda package for your system into your $HOME folder. See https://www.continuum.io/downloads#linux for more information.

# Download 64-bit installation
wget https://repo.continuum.io/archive/Anaconda2-4.2.0-Linux-x86_64.sh -O ~/anaconda.sh

# Download 32-bit installation
wget https://repo.continuum.io/archive/Anaconda2-4.2.0-Linux-x86.sh -O ~/anaconda.sh

Step 1c: Change directory cd into the location of the downloaded shell (.sh) file from Continuum and run the command below.

# Install and add prefix
bash ~/anaconda.sh -b -p $HOME/anaconda

# Add Anaconda to PATH
export PATH="$HOME/anaconda/bin:$PATH"

Step 1d: Once Anaconda has been installed, restart Terminal and run the command below to verify that Anaconda was properly installed.

anaconda --version
#> anaconda Command line client (version 1.4.0)

Step 2. Create a Virtual Environment and Install QIIME

After Anaconda has been installed, we can now proceed to create a virtual environment which will allow you to keep tools and dependencies separate from your systems so you do not cause any conflicts with other programs. See http://qiime.org/install/install.html for more information.

Step 2a: Create a virtual environment named qiime191 and install the basic QIIME package

conda create --yes -c bioconda -n qiime191 python=2.7 qiime matplotlib=1.4.3 mock nose

Step 2b: Actiate the environment and install the additional components required for all OTU-picking methods and Chimera removal.

# Activate qiime environment
source activate qiime191 

# Add additional channels for required packages
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda config --add channels biocore
conda config --add channels hcc 

# Install additional packages
conda install --yes \
r-essentials \
blast-legacy \
cd-hit \
cdbtools \
cogent \
ea-utils \
infernal \
microbiomeutil \
muscle \
mothur \
r-vegan \
sourcetracker \
sortmerna \
sumaclust \
rdp-classifier \
swarm \
tax2tree

Step 3. Test Installation for any Missing Dependencies

The final step is to verify that all the required tools are properly installed for use with a complete QIIME workflow. To do this, we can use an internal command to verify that each of the required dependencies can be found.

# Activate environment
source activate qiime191

# Print QIIME configuration status
print_qiime_config.py -tf