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.
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.
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
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
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-3.4). If not, install PIP by the official instructions
Upgrade to the newest version can be done also using PIP.
pip install --upgrade rnftools
To install RNFtools directly from GIT repository, run
git clone git://github.com/karel-brinda/rnftools pip install rnftools
pip install git+http://github.com/karel-brinda/rnftools
First, we need to create a directory where RNFtools will be installed.
Then we have to add its path into the variable
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
export PYTHONUSERBASE=~/rnftools export PATH=$PATH:~/rnftools/bin