Installation

OSTIR is a Python module and associated command line script. We recommend installing OSTIR using Bioconda on Linux or macOS. This will automatically install OSTIR and all of its dependencies, including ViennaRNA and the required Python modules.

Method 1. Install using Bioconda (recommended; Linux, macOS)

• Install the conda package manager. One way to do this is by installing Miniconda.
• Run conda install -c bioconda ostir
• Run ostir to check that it is installed and see the help.

Method 2. Install using Pip (for experts; Linux, macOS, Windows)

• Download and install ViennaRNA on your own and add it to your $PATH.
• Run pip install ostir
• Run ostir to check that it is installed and see the help.

Method 3. Install from Source Code (for developers; Linux, macOS, Windows)

• Activate a conda environment that has ViennaRNA installed or download and install ViennaRNA on your own and add it to your $PATH.
• Clone this repository
• Navigate to the ./ostir/ directory
• Install/update the necessary packaging tools with python3 -m pip install --user --upgrade setuptools wheel
• Package the code with python3 setup.py sdist bdist_wheel
• Install the package with python3 -m pip install ./
• To test your install run python -m unittest