QIIME Install in Ubuntu Linux

This guide was tested using the Long Term Support (LTS) version of Ubuntu (10.04); due to library incompatibilities in Ubuntu 11.10 these instructions will not work and most non-deb-package installs will fail, thus we do not recommend trying native installs either. Note that you might be able to install in other Linux distributions following these instructions.

Installing QIIME in Ubuntu LTS (10.04)

1. Install Ubuntu 10.04 in your prefered way.
2. Install the building dependencies in your machine. This step requires admin (sudo) access. If you do not have sudo access, you must ask your system administrator to grant you sudo access, or to run these steps for you. In general, all of this software should already be installed but it may not be. It’s therefore best to run this command before the following step.

sudo apt-get --force-yes -y install libgsl0-dev openjdk-6-jdk libxml2 libxslt1.1 libxslt1-dev ant subversion build-essential zlib1g-dev libpng12-dev libfreetype6-dev mpich2 libreadline-dev gfortran unzip libmysqlclient16 libmysqlclient16-dev ghc

3. Run the following commands. In this example the software will be installed in your home directory under the qiime_software folder, you can replace this with any path you want.

mkdir $HOME/qiime_software/
wget http://bmf.colorado.edu/QIIME/app-deploy-qiime-1.4.0.tgz
tar zxvf app-deploy-qiime-1.4.0.tgz
cd app-deploy-qiime-1.4.0
python app-deploy.py $HOME/qiime_software/ -f etc/qiime_1.4.0.conf

4. Happy QIIME-ing!