2.1. Installation

RNFtools is distributed as a Python-based package, which is distributed through BioConda (a bioinformatics channel for the Conda package manager) and PIP. Since BioConda does not require a root account and installs also all the RNFtools dependencies, it is the recommended way of installation.

Contents

• Installation
  • Requirements
  • Installation using Bioconda (recommended)
  • Installation using PIP from PyPI
  • Installation using PIP from GIT
  • Installation using PIP without a root account

2.1.1. Requirements

Requirements for basic installation of RNFtools are:

• Unix-like operating system (Linux, OS X, etc.).
• Python 3.3+.

When RNFtools is installed using BioConda, all the additional dependencies are installed automatically. If not, installation of the following programs is up to user.

• Art
• CuReSim
• DWGsim
• Mason
• WGsim
• SamTools

2.1.2. Installation using Bioconda (recommended)

The easiest and safest approach of RNFtools installation is to create a separate Bioconda environment.

conda create -n rnftools rnftools

Once the environment is installed, you can activate it by

source activate rnftools

and deactivate by

source deactivate

Alternatively, RNFtools can be installed directly in the default Conda environment. However, this approach might not work in certain situations due to possible collisions with the dependencies of your already installed packages.

conda install rnftools

2.1.3. Installation using PIP from PyPI

RNFtools can be installed using PIP from PyPI by

pip install rnftools

If this command does not work, check if pip is installed in your system (the command may have a slightly different name, e.g., pip, pip-3, pip.4, pip-3.4). If not, install PIP by the official instructions (or try easy_install3 pip).

Upgrade to the newest version can be done also using PIP.

pip install --upgrade rnftools

2.1.4. Installation using PIP from GIT

To install RNFtools directly from GIT repository, run

git clone git://github.com/karel-brinda/rnftools
pip install rnftools

or

pip install git+http://github.com/karel-brinda/rnftools

2.1.5. Installation using PIP without a root account

First, we need to create a directory where RNFtools will be installed.

mkdir ~/rnftools

Then we have to add its path into the variable PYTHONUSERBASE

export PYTHONUSERBASE=~/rnftools

Now we can finally install RNFtools. The parameter --user implies installation into the predefined directory.

pip install --user rnftools

As the last step, we need to add the following lines to ~/.bashrc

export PYTHONUSERBASE=~/rnftools
export PATH=$PATH:~/rnftools/bin