Detailed installation

For someone who doesn’t use Python, the easiest way to install tiara is to use a conda environment. This way your existing Python-dependent programs won’t be affected by, for example, updating some libraries.

Python installation

1. Follow the installation instruction for your OS on: https://docs.conda.io/en/latest/miniconda.html. Install Python >=3.7 version. (Most tested on 3.8).

2. After you installed (mini)conda and verified it works, create new virtual environment, for example tiara-env:

    conda create --name tiara-env python=3.8
   

3. After the environment is crated, run conda activate tiara-env.

You can of course install tiara in any Python environment (venv, virtualenv etc), but it should be a fresh one.

Tiara installation

Using pip

Run pip install tiara, preferably in a fresh environment.

Using conda

Run conda install -c conda-forge tiara, preferably in a fresh environment.

We recommend to use mamba instead of conda (it’s faster).

Unfortunately currently it does work only for python 3.7 and 3.8.

Using setup.py

Now you can install tiara in your environment. There are two ways to handle dependencies:

• You can install them by hand: in the tiara-env run conda install numpy pytorch numba joblib and then conda install -c conda-forge tqdm biopython skorch. (Or just simply pip install -r requirements.txt)
• You can let the setup.py script install them for you. It could potentially cause problems with your conda environment though, but if you use it only for tiara, everything should be fine. This is a recommended option.

Now you can either clone https://github.com/ibe-uw/tiara.git or download the latest release from https://github.com/ibe-uw/tiara/releases, navigate to the directory containing setup.py and run it:

git clone https://github.com/ibe-uw/tiara.git
cd tiara
python setup.py install

Verify the installation with tiara-test (it may take a while).

Back to README