Installation¶

Prerequisites¶

OmicVerse can be installed via conda or pypi and you need to install pytorch at first

Note

To avoid potential dependency conflicts, installing within a conda environment is recommended. And using pip install -U omicverse to update.

Platform¶

In different platform, there are some differences in the most appropriate installation method.

Windows: You need to install the wsl subsystem and conda in the wsl subsystem to configure the omicverse environment.
Linux: We can choose to install anaconda or miniconda, and then use conda to configure the omicverse environment
Mac Os: We recommend using miniforge or mambaforgeto configure.

pip prerequisites¶

If using conda/mamba, then just run conda install -c anaconda pip and skip this section.
Install Python, we prefer the pyenv version management system, along with pyenv-virtualenv.

Apple silicon prerequisites¶

Installing omicverse on a Mac with Apple Silicon is only possible using a native version of python. A native version of python can be installed with an Apple Silicon version of mambaforge (which can be installed from a native version of homebrew via brew install --cask mambaforge).

One-click installation¶

Note

This part of the code installation may be wrong, if you encounter version error please refer to the following detailed code for step-by-step installation

conda create -n omicverse python=3.10
conda activate omicverse
conda install mamba -c conda-forge
mamba install jax jaxlib -c conda-forge
pip3 install torch torchvision torchaudio
pip3 install torch_geometric
pip3 install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.3.0+cu121.html
pip3 install -U omicverse

Note that the version of torch we installed is 2.3.0

Conda¶

1. Install conda. We typically use the `mambaforge` distribution. Use python>=3.8, conda consider using `mamba` instead of `conda`.¶

2. Create a new conda environment:¶

conda create -n omicverse python=3.10

3. Activate your environment:¶

conda activate omicverse

4. Install PyTorch and PyG at first:¶

If you want to install the previous version of pytorch, please check out the tutorials of https://pytorch.org/get-started/previous-versions/

# Nigntly version
conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia
# CPU only
# conda install pytorch torchvision torchaudio cpuonly -c pytorch
# Previous version
# conda install pytorch==1.13.1 torchvision==0.14.1 torchaudio==0.13.1 -c pytorch
conda install pyg -c pyg

5. Install `omicverse`:¶

conda install omicverse -c conda-forge

Pip¶

The omicverse package can be installed via pip using one of the following commands:

1. Install PyTorch at first: More about the installation can be found at PyTorch.¶

# ROCM 5.7 (Linux only)
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/rocm5.7
# CUDA 11.8
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
# CUDA 12.1
pip3 install torch torchvision torchaudio
# CPU only
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu

2. You also need to install PyG ¶

pip install torch_geometric
# Optional dependencies:
# CUDA 11.8
#pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.1.0+cu118.html
# CPU only
#pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.1.0+cpu.html

3. You need to configure the gcc to install some package¶

#ubuntu
sudo apt update
#install build-essential
sudo apt install build-essential

#centos
sudo yum group install "Development Tools"

if you can see the version of gcc, it means the success of installation

gcc --version

4. After the installation of pytorch, we can start to install `omicverse` by `pip`¶

Warning

If you live in mainland China, you can try adding -i after pip https://pypi.tuna.tsinghua.edu.cn/simple. Likes, pip install -U omicverse -i https://pypi.tuna.tsinghua.edu.cn/simple

pip install -U omicverse
pip install -U numba

5. If you want to using Nightly verseion. There are two ways for you to install¶

Nightly version - clone this repo and run: pip install .
Using pip install git+https://github.com/Starlitnightly/omicverse.git

Others¶

Warning

If you're getting errors with pip, then for packages that pip can't install, such as scikit-misc, you can use conda install scikit-misc -c conda-forge -c bioconda to install them, and then continue to use pip to install the original packages after that

if you using M1/M2 silicon, perhaps the following code will be helped:

#python 3.9
conda install s_gd2 -c conda-forge
pip install -U omicverse 
conda install pytorch::pytorch torchvision torchaudio -c pytorch

[Extra] GPU-accelerated¶

The easiest way to install rapids-singlecell and omicverse is to use one of the yaml file provided in the conda folder. These yaml files install everything needed to run the example notebooks and get you started.

conda env create -f conda/omicverse_gpu.yml
# or
mamba env create -f conda/omicverse_gpu.yml

Jupyter-lab¶

For the best interactive analysis experience, we highly recommend installing jupyter-lab so that you can interactively edit the code and get the analysis results and visualizations right away.

pip install jupyter-lab

After you have finished the installation, in your terminal (note that you must be in the omicverse environment, not the base environment), type jupyter-lab, a URL will appear, we can open this URL in the browser to start our analysis journey!

Development¶

For development - clone this repo and run:

pip install -e ".[dev,docs]"