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Install QIIME 1

update 2018: consider using the new version  → QIIME 2

Install QIIME-1.9.1 using conda (Ubuntu / Linux)

1) Install Miniconda
bash # run installation
2) Install QIIME
conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
conda install psutil

# test QIIME installation
conda activate qiime1 -t
# Start QIIME
conda activate qiime1

# Finish QIIME
conda deactivate

Install GNU R and additional packages required for QIIME

→ DESeq2 (required in
→ CSS (required in

# install fastq-join (ea-utils) required for qiime
sudo apt-get install ea-utils  # Ubuntu/Linux (or, compile using make)

Install QIIME in Virtual Machine (Windows)

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

# activate virtual machine