Installation

The ADEPT package is developed based on the pytorch and pytorch-geometric framework and can be implemented on both GPU and CPU. We recommend running the package on GPU. Please ensure that pytorch and cudnn are installed correctly. To run ADEPT, all dependencies included in the file ‘requirement.txt’ need to be installed. We highly recommend to install ADEPT with Anaconda.

Anaconda

For convenience, we suggest using a separate conda environment for running ADEPT. Please ensure anaconda3 is installed.

Create conda environment and install MaskGraphene package.

### Installation from github
1. git clone --recursive https://github.com/maiziezhoulab/AquilaDeepFilter.git

2. conda create -n [EnvName] python=3.7

3. source activate [EnvName]

4. install pytorch (https://pytorch.org/get-started/locally/) + pytorch-geometric (https://pytorch-geometric.readthedocs.io/en/latest/install/installation.html) before everything

5. pip install -r requirements.txt

6. pip install scanpy python-igraph rpy2

7. install.packages("mclust") with R

Google Colab

Colab user can link to google drive and enter the folder through code below：

from google.colab import drive
drive.mount('/content/drive')

# Modify it to the name you saved for the fold with
folder_name = 'ADEPT/'
import sys
sys.path.append('/content/drive/My Drive/{}'.format(folder_name))

%cd /content/drive/My\ Drive/$folder_name

In colab environment (with complete base env), you need to install libraries below:

!pip install torch-geometric
!pip install -r requirements.txt
!pip install scanpy
!pip install python-igraph
!pip install rpy2

import torch
!pip install torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-{torch.__version__}.html

import rpy2.robjects as robjects

install_cmd = "install.packages('mclust', repos='http://cran.r-project.org')"
robjects.r(install_cmd)

For possible error, please try:

"""
   OSError: cannot load library 'C:\Program Files\R\R-4.3.1\bin\x64\R.dll':error 0x780
"""
import os
os.environ['R_HOME'] = 'C:\\Program Files\\R\\R-4.3.1\\' # replace it with your own path

This serves as an example for installing ADEPT with certain cuda version. However, one might need to adapt to a proper version combination of these packages to make the env runnable.