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Install

Install QIIME-1.9.1 using conda (Ubuntu / Linux)


1) Install Miniconda
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod u+x ./Miniconda2-latest-Linux-x86_64.sh   # give permission
./Miniconda2-latest-Linux-x86_64.sh # run installation

# add path to your .bashrc file, if not already done
export PATH="/home/username/miniconda2/bin:$PATH"

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
source activate qiime1
print_qiime_config.py -t


# Start QIIME
source activate qiime1

# Finish QIIME
source deactivate

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 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



Subpages (2): R for QIIME usearch61