Installation

This section describes how to install HTSinfer, either from Bioconda (recommended for most users) or GitHub (for experienced users and developers).

Both installation methods require the popular package and environment manager Conda to be available on your system.

Note

For improved performance, we recommend using Conda’s drop-in replacement Mamba instead. In that case, simply replace conda with mamba in all of the commands below.

Install from Bioconda

The easiest and quickest installation method is to install the latest HTSinfer release from Bioconda.

To install HTSinfer in your currently active environment, run:

conda install bioconda::htsinfer

Note

We do not recommend installing HTSinfer into the default (base) environment. Instead, activate a project- or tool-specific environment with conda activate MY_CONDA_PROJECT. If you do not have such an environment, just create one with conda create --name MY_CONDA_PROJECT. MY_CONDA_PROJECT can be any name you like (with some constraints imposed by Conda), e.g., htsinfer.

Install from GitHub

If you wish to use the latest unreleased version of the tool or if you would like to contribute to its further development, please install HTSinfer from GitHub.

First clone the repository:

git clone https://github.com/zavolanlab/htsinfer.git
cd htsinfer

Then, install HTSinfer and its dependencies via Conda:

conda env create --file environment.yml

Alternatively, to include HTSinfer’s optional development dependencies, run the following instead:

conda env create --file environment-dev.yml

After the installation is complete, activate the htsinfer Conda environment with:

conda activate htsinfer

If you have installed the development dependencies, you can verify that HTSinfer was installed correctly by executing the tests shipped with the package:

python -m pytest