Conda Installation

SCALT is written in python, R and bash programming language. To ensure the adaptability accross different operating systems, SCALT requires the installation of a Conda environment. Conda is a powerful command line tool for package and environment management that runs on Windows, macOS, and Linux.

To install Conda, visit the Conda Installation Page and follow the instructions step by step for the regular installation on your operating system.

SCALT download

Subsequent to the installation of conda, make sure that conda is activated with the following command:

conda activate

Then, download SCALT either from the following Github repository as a zipped file or directly using the following command on the command line:

git clone https://github.com/danitrave/SCALT.git

Move to the SCALT directory making use of cd command as follows:

cd path/to/directory/SCALT

Inside the directory, the configuration file SCALT_conda_envSetup.yml enables the installation of the proper SCALT environment in which all the packages and programs required for the tool are provided. Install the environment running the following command:

conda env create -f SCALT_conda_envSetup.yml

Finally, make sure to activate the environment if not already activated using the following commad:

conda activate SCALT

Now, you are ready to play with SCALT!