Install QIIME 1
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
# 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 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