Installation¶
Geomosaic has been designed to be straightforward to install and execute on Linux workstations and High-Performance Computing (HPC) systems.
New to metagenomics? Geomosaic automatically creates the workflow, Conda environments, and HPC execution scripts, so you can get started without manually connecting dozens of independent software packages.
The current installation method uses a Conda environment that automatically installs all required software dependencies. Once installed, Geomosaic can generate complete workflows and execution scripts without requiring manual installation of individual bioinformatics packages.
Note
A Conda package for Geomosaic is currently under development and will simplify the installation process in future releases.
Step 1 - Clone the repository¶
Clone the Geomosaic repository and move into the project directory.
git clone https://github.com/giovannellilab/Geomosaic.git
cd Geomosaic
All subsequent installation steps should be performed from within the cloned repository.
Step 2 - Install conda environment¶
We recommend using mamba instead of Conda because it resolves package dependencies considerably faster.
mamba env create -f environment.yaml
conda env create -f environment.yaml
Now the geomosaic environment can be activated
conda activate geomosaic
Step 3 - Install the geomosaic package in the python environment¶
pip install .
Verify the installation¶
To verify that the installation completed successfully, run:
geomosaic --help
If the installation was successful, the Geomosaic command-line interface and the list of available commands will be displayed.