Installation Guide 🦮#

Important

Supported Python versions are 3.10, 3.11 and 3.12

Latest version#

Installation via Conda (recommended) 🐍#

The recommended way to install PANORAMA is via Conda from the Bioconda channel. We recommend creating a new Conda environment for PANORAMA to prevent any conflicts with other packages.

# Create a new Conda environment and install PANORAMA in one line:
conda create -n panorama -c conda-forge -c bioconda panorama

# Activate the environment
conda activate panorama

# Check the install
panorama --version

If you want to use a specific version of PANORAMA, you can install it with:

# X.X.X is the version number
conda create -n panorama -c conda-forge -c bioconda panorama==X.X.X

To use a specific python version:

# X.X.X is the version number
conda create -n panorama -c conda-forge -c bioconda panorama python=X.X

Installing from source code (GitHub) 🐙#

Within a Conda environment 🐍#

1. Clone the GitHub Repository#

git clone https://github.com/labgem/PANORAMA.git
cd PANORAMA

2. Create and Configure the Conda Environment#

conda create -n panorama
conda config --add channels bioconda
conda config --add channels conda-forge
conda env update -n panorama --file panorama.yml
conda activate panorama

Alternatively, in one line:

conda env create -f panorama.yml # -n panorama ## if you want to name the environment differently
conda activate panorama

3. Install PANORAMA#

pip install .

4. Test the Installation#

panorama --help
panorama --version

Manual Installation (without Conda) 🛠️#

Important

PANOARMA requires Python 3.10 or higher.

1. Clone the Repository#

git clone https://github.com/labgem/PANORAMA.git
cd PANORAMA

2. Install PANORAMA Dependencies#

Install MMSeqs2 (≥ 13.45111) manually:

With Homebrew: brew install mmseqs2
On Debian-based systems: sudo apt install mmseqs2

Note

Here is the complete installation guide of MMSeqs2: soedinglab/MMseqs2

3. Install PANORAMA and Python Dependencies#

Dependencies are declared in the pyproject.toml file:

pip install --upgrade pip setuptools build wheel
pip install .

Warning

geckodriver is not compatible with pip, so the feature that generate png image from bokeh is not supported.

Development Version#

1. Get the Development branch#

To clone the dev Branch

git clone --branch dev https://github.com/labgem/PANORAMA.git

2. Install Dependencies#

Follow the same steps as in the standard installation. With a conda environment or with a manual installation.

3. Install the Development Version#

pip install .

Troubleshooting#

If you encounter any problems, please check the known issues below. If you still can’t solve your problem, please open an issue on GitHub.