update 2018: consider using the new version → QIIME 2

Install QIIME-1.9.1 using conda (Ubuntu / Linux)

1) Install Miniconda

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

bash Miniconda2-latest-Linux-x86_64.sh # run installation

http://conda.pydata.org/miniconda.html

2) Install QIIME

conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda

conda install psutil

→ PackagesNotFoundError (2019)

# test QIIME installation

conda activate qiime1

print_qiime_config.py -t

→ Edit .qiime_config

# Start QIIME

conda activate qiime1

# Finish QIIME

conda deactivate

http://qiime.org/install/install.html

Install GNU R and additional packages required for QIIME

→ DESeq2 (required in differential_abundance.py)

→ CSS (required in normalize_table.py)

# install fastq-join (ea-utils) required for qiime multiple_join_paired_ends.py

sudo apt-get install ea-utils # Ubuntu/Linux (or, compile using make)

→ install usearch

Install QIIME in Virtual Machine (Windows)

# download and decompress latest version of → QIIME Virtual Box image

wget ftp://ftp.microbio.me/pub/qiime-release-VMs/QIIME-1.9.1-amd64.vdi.gz

# activate virtual machine

http://qiime.org/install/virtual_box.html