Installation¶

Pegasus works with Python 3.6, 3.7, and 3.8.

Linux¶

Ubuntu/Debian¶

Prerequisites¶

On Ubuntu/Debian Linux, first install the following dependency by:

sudo apt install build-essential

Next, you can install Pegasus system-wide by PyPI (see Ubuntu/Debian install via PyPI), or within a Miniconda environment (see Install via Conda).

To use the Force-directed-layout (FLE) embedding feature, you’ll need Java. You can either install Oracle JDK, or install OpenJDK which is included in Ubuntu official repository:

sudo apt install default-jdk

Ubuntu/Debian install via PyPI¶

First, install Python 3 and pip tool for Python 3:

sudo apt install python3 python3-pip
python3 -m pip install --upgrade pip

Now install Pegasus via pip:

python3 -m pip install pegasuspy

There are optional packages that you can install:

mkl: This package improves math routines for science and engineering applications:
```
python3 -m pip install mkl
```
fitsne: This package is to calculate t-SNE plots using a fast algorithm FIt-SNE:
```
sudo apt install libfftw3-dev
python3 -m pip install fitsne
```
leiden: This package provides Leiden clustering algorithm, besides the default Louvain algorithm in Pegasus:
```
python3 -m pip install leidenalg
```

Fedora¶

Prerequisites¶

On Fedora Linux, first install the following dependency by:

sudo dnf install gcc gcc-c++

Next, you can install Pegasus system-wide by PyPI (see Fedora install via PyPI), or within a Miniconda environment (see Install via Conda).

To use the Force-directed-layout (FLE) embedding feature, you’ll need Java. You can either install Oracle JDK, or install OpenJDK which is included in Fedora official repository (e.g. java-latest-openjdk):

sudo dnf install java-latest-openjdk

or other OpenJDK version chosen from the searching result of command:

dnf search openjdk

Fedora install via PyPI¶

Fedora 33+ has set Python 3.9 as the default Python 3 version. However, Pegasus has not supported it yet. So we’ll use Python 3.8 in this tutorial.

First, install Python 3 and pip tool for Python 3:

sudo dnf install python3.8
python3.8 -m ensurepip --user
python3.8 -m pip install --upgrade pip

Now install Pegasus via pip:

python3.8 -m pip install pegasuspy

There are optional packages that you can install:

mkl: This package improves math routines for science and engineering applications:
```
python3.8 -m pip install mkl
```
fitsne: This package is to calculate t-SNE plots using a faster algorithm FIt-SNE:
```
sudo dnf install fftw-devel
python3.8 -m pip install fitsne
```
leiden: This package provides Leiden clustering algorithm, besides the default Louvain algorithm in Pegasus:
```
python3.8 -m pip install leidenalg
```

macOS¶

Prerequisites¶

First, install Homebrew by following the instruction on its website: https://brew.sh/. Then install the following dependencies:

brew install libomp

And install macOS command line tools:

xcode-select --install

Next, you can install Pegasus system-wide by PyPI (see macOS installation via PyPI), or within a Miniconda environment (see Install via Conda).

To use the Force-directed-layout (FLE) embedding feature, you’ll need Java. You can either install Oracle JDK, or install OpenJDK via Homebrew:

brew cask install java

macOS install via PyPI¶

You need to install Python and pip tool first:

brew install python3
python3 -m pip install --upgrade pip

Now install Pegasus:
```
python3 -m pip install pegasuspy
```

There are optional packages that you can install:

mkl: This package improves math routines for science and engineering applications:
```
python3 -m pip install mkl
```
fitsne: This package is to calculate t-SNE plots using a faster algorithm FIt-SNE. First, you need to install its dependency fftw:
```
brew install fftw
```

Then install fitsne by:

python3 -m pip install fitsne

leiden: This package provides Leiden clustering algorithm, besides the default Louvain algorithm in Pegasus:
```
python3 -m pip install leidenalg
```

Install via Conda¶

Alternatively, you can install Pegasus via Conda, which is a separate virtual environment without touching your system-wide packages and settings.

You can install Anaconda, or Miniconda (a minimal installer of conda). In this tutorial, we’ll use Miniconda.

Download Miniconda installer for your OS. For example, if on 64-bit Linux, then use the following commands to install Miniconda:

export $CONDA_PATH=/home/foo
bash Miniconda3-latest-Linux-x86_64.sh -p $CONDA_PATH/miniconda3
mv Miniconda3-latest-Linux-x86_64.sh $CONDA_PATH/miniconda3
source ~/.bashrc

where /home/foo should be replaced by the directory to which you want to install Miniconda. Similarly for macOS.

Create a conda environment for pegasus. This tutorial uses pegasus as the environment name, but you are free to choose your own:
```
conda create -n pegasus -y python=3.8
```

Also notice that Python 3.8 is used in this tutorial. To choose a different version of Python, simply change the version number in the command above. Since Pegasus conda package only support Python 3.7 and 3.8 for now, you should choose your Python version from either of these two.

Enter pegasus environment by activating:
```
conda activate pegasus
```
Install Pegasus:
```
conda install -y -c bioconda pegasuspy
```

Install via Singularity¶

Singularity is a container engine similar to Docker. Its main difference from Docker is that Singularity can be used with unprivileged permissions.

On Singularity Hub, we maintain Singularity container of Pegasus current stable version (running on Ubuntu Linux 20.04 with Python 3.8). On your server or machine where Singularity has been installed, pull this container using:

singularity pull shub://klarman-cell-observatory/pegasus

This will fetch a 2.4GB container file pegasus_latest.sif on your machine. Then interact with it, e.g.:

singularity run pegasus_latest.sif

Please refer to Singularity image interaction guide for details.

Development Version¶

To install Pegasus development version directly from its GitHub respository, please do the following steps:

Install prerequisite libraries as mentioned in above sections.
Install Git. See here for how to install Git.

Use git to fetch repository source code, and install from it:

git clone https://github.com/klarman-cell-observatory/pegasus.git
cd pegasus
pip install -e .

where -e option of pip means to install in editing mode, so that your Pegasus installation will be automatically updated upon modifications in source code.