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
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.
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