Installation¶

tribal can be installed via bioconda (coming soon) or github and can be run as a python package or via the command line.

Dependencies¶

tribal has the following dependencies:

    python >=3.9,<3.11
    numpy >=1.26,<2.0
    pandas
    networkx >=3.1
    pygraphviz >=1.10
    ete3 >=3.1.2
    mafft ==7.526
    glpk >=5.0
    pyomo >=6.7
    biopython >=1.81

tribal can be installed from Github or from bioconda. We recommend installing from bioconda.

Installing from bioconda (recommended)¶

conda create -n tribal -c bioconda tribal
conda activate tribal

See Veryifing installation to make sure the package was installed correctly.

Installing from GitHub¶

git clone https://github.com/elkebir-group/TRIBAL.git
cd TRIBAL

Dependencies can be installed using a package mangager such as conda, mamba or micromamba, using the included tribal.yml file.

conda env create -f tribal.yml

To build and install tribal into this environment, follow the instructions below:

conda activate tribal
python -m build 
pip install dist/tribal-0.1.0-py3-none-any.whl

dnapars is a requirement to run the preprocessing tools. The source code is included in the package and can be installed using the dnapars_install.sh script.

chmod +x dnapars_install.sh
./dnapars_install.sh

Verifying installation¶

tribal can be imported as a package or run via a command line interface.

To verify the package can be imported, run the following in the terminal.

python -c "import tribal"

See Package Overivew for more detailed usage intstructions.

To verify the CLI tool was properly installed, run the following in the terminal.

tribal --help

See Command Line Interface for more detailed usage intstructions.