Miniconda

Sometimes you want complete control on your Python installation rather than rely on the packages and versions provided for you by the central installed python installation. This page will guide you in the process of installing miniconda on your home account. We describe here how to download, install and update a miniconda installation that will give you complete control on the packages that you have and the pace on which those packages will be updated.

Downloading Miniconda

Miniconda can be downloaded from:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

No installing anything

Just load the module:

module purge
module load genomics/qiime

This module will load python 2.7.3 and qiime on top of that

Installing QIIME on a virtual environment on top of python 2.7.13

Use this:

module purge
module load compilers/python/2.7.13

virtualenv veqiime
cd veqiime
source ./bin/activate
pip install numpy
pip install qiime (this step takes around a minute)

After installation all that you have to do is:

module load compilers/python/2.7.13
cd veqiime
source ./bin/activate

and qiime is ready for use.

Installing QIIME on top of python 2.7.13 (No virtual env)

Execute:

module purge module load compilers/python/2.7.13

pip install qiime --user

In this case qiime will be installed locally on your home directory at:

~/.local/lib/python2.7/site-packages

All that you have to do is:

module load compilers/python/2.7.13

And qiime is ready for use.

Installing with Miniconda

First install miniconda following the instructions:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86\_64.sh
source ~/.bashrc

conda install numpy

conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda

Finally follow the instructions at the end of the installation

To activate this environment, use:

> source activate qiime1

To deactivate this environment, use:

> source deactivate qiime1