# 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](https://docs.conda.io/en/latest/miniconda.html) 
from the [Bioconda](https://bioconda.github.io/) channel.
We recommend creating a new Conda environment for PANORAMA to prevent any conflicts with other packages.

```shell
# 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:
```shell
# 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:
```shell
# 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) 🐙
(with_conda_env)=
#### Within a Conda environment 🐍

##### 1. Clone the GitHub Repository

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

##### 2. Create and Configure the Conda Environment

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

##### 3. Install PANORAMA

```shell
pip install .
```

##### 4. Test the Installation

```shell
panorama --help
panorama --version
```

#### Manual Installation (without Conda) 🛠️

```{important}
PANOARMA requires Python 3.10 or higher.
```

##### 1. Clone the Repository

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

##### 2. Install PANORAMA Dependencies

Install **MMSeqs2 (≥ 13.45111)** manually:

* With [Homebrew](https://github.com/Homebrew/brew): `brew install mmseqs2`
* On Debian-based systems: `sudo apt install mmseqs2`

```{note}
Here is the complete installation guide of MMSeqs2: 
[https://github.com/soedinglab/MMseqs2/wiki#installation](https://github.com/soedinglab/MMseqs2/wiki#installation)
```

##### 3. Install PANORAMA and Python Dependencies

Dependencies are declared in the `pyproject.toml` file:

```shell
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

```shell
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](#with_conda_env) or with a [manual installation](#manual-installation-without-conda).

### 3. Install the Development Version
```shell
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](https://github.com/labgem/PANORAMA/issues).