Installing QIIME-1.9.1 on CentOS 6.5 (By Yue Zheng)


QIIME consists of native Python 2 code and additionally wraps many external applications. As a consequence of this pipeline architecture, QIIME has a lot of dependencies and can be very challenging to install.

1. Setting up qiime-deploy on CentOS

1.1 sudo vim /etc/yum.repos.d/zeromq.repo

Paste the following into that file:

name=The latest stable of zeromq builds (CentOS_CentOS-6)

Save and exit that file

1.2 Install the qiime-deploy dependencies on your machine

sudo yum groupinstall -y "development tools"
sudo yum install -y ant compat-gcc-34-g77 java-1.6.0-openjdk java-1.6.0-openjdk-devel freetype freetype-devel zlib-devel mpich2 readline-devel zeromq zeromq-devel gsl gsl-devel libxslt libpng libpng-devel libgfortran mysql mysql-devel libXt libXt-devel libX11-devel mpich2 mpich2-devel libxml2 xorg-x11-server-Xorg dejavu* python-devel sqlite-devel tcl-devel tk-devel R R-devel ghc

2. Installing requisite Python and R packages

# Installing sqlite-devel
sudo yum install sqlite-devel –y

# Installing Python 2.7
tar xf Python-2.7.8.tgz
cd Python-2.7.8
./configure --prefix=/usr
make && make install

# Install setuptools & pip
# First get the setup script for Setuptools:
# Then install it for Python 2.7 :
sudo python2.7
# Now install pip using the newly installed setuptools:
sudo easy_install-2.7 pip
# With pip installed you can now do things like this:
pip2.7 install [packagename]

# Install virtualenv for Python 2.7
sudo pip2.7 install virtualenv

# Check the system Python interpreter version
python --version
# This will show Python 2.7.8

# Maybe you will found yum can not be used this moment, because yum is associated with python2.6. Thus, we modified the yum conf files to use python2.6
sudo vim /usr/bin/yum
# Replace “#!/usr/bin/python” by “#!/usr/bin/python2.6”
# Installing R packages
# Run R and execute the following commands
install.packages(c('ape', 'biom', 'optparse', 'RColorBrewer', 'randomForest', 'vegan'))
biocLite(c('DESeq2', 'metagenomeSeq'))

3. Install the latest QIIME release and its base dependencies is with pip

sudo pip2.7 install numpy
sudo pip2.7 install qiime -v
# For Chines user, you may find the suspend of pip, as the limitation of network. For example, If FastTree cannot be download, you can download it by another port of internet, and then post the install package into your local address. Next step, Downloading the qiime-1.9.1.tar.gz and changing the description of FastTree in After you modified the qiime-1.9.1.tar.gz you can post it into your local address. Finally, run sudo pip2.7 install qiime –v –i [local address]

# Installing QIIME 1.9.0's dependencies
# Downloading the zip packages of ‘qiime deploy’ and ‘qiime deploy conf’ from Github
mkdir ~/qiime_software
cd qiime-deploy-master
sudo python2.7 ~/qiime_software/ -f ~/qiime-deploy-conf/qiime/qiime-1.9.1/qiime.conf --force-remove-failed-dirs
# After this step, it will display the list including ‘Packages deployed successfully’, ‘Packages skipped’ and ‘Packages failed to deply’
source ~/qiime_software/ –tf

# If there are some packages were uninstalled, you should install them manually
# For example, usearch and amplicannoise were failed to install.

# Installing usearch manually
# Visting to download the USEARCH v5.2.236
# Moving the binary file into /usr/bin and change the name as usearch, then chmod 755 [the binary file] 

# Installing usearch manually
# Downloading the AmpliconNoiseV1.27.tar.gz
tar -xvzf AmpliconNoiseV1.27.tar.gz
cd AmpliconNoiseV1.27
make clean
make install
echo "export PATH=$HOME/AmpliconNoiseV1.27/Scripts:$HOME/AmpliconNoiseV1.27/bin:$PATH" >> $HOME/.bashrc
echo "export PYRO_LOOKUP_FILE=$HOME/AmpliconNoiseV1.27/Data/LookUp_E123.dat" >> $HOME/.bashrc
echo "export SEQ_LOOKUP_FILE=$HOME/AmpliconNoiseV1.27/Data/Tran.dat" >> $HOME/.bashrc

# PATH Environment Variable
echo "export PATH=$HOME/bin/:$PATH" >> $HOME/.bashrc
source $HOME/.bashrc

# Finnaly verification
source ~/qiime_software/ –tf


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