Chapter 2 Prerequisites

For reproducing the tutorials in the modules 4.2 and 5, we need a few R packages and a Python package. Detailed instructions are below.

2.1 R packages

For module 4.2, we need reticulate to import the Python package (see next section. You can install it within R:
```
# install reticulate for module 4.2
install.packages("reticulate")
```

For module 5.1, we need cardelino, which is only available at GitHub, so we need to use devtools:

# install devtools for module 5.1
install.packages('devtools')

# install cardelino for module 5.1
devtools::install_github("single-cell-genetics/cardelino", build_vignettes = FALSE)

For module 5.2, we need infercnv, which requires a standalone software JAGS. Please install JAGS manually for Windows or Mac from this link before install rjags R package: https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/
Continue and install rjags and infercnv:
```
# install rjags for module 5.2
install.packages('rjags')
```
```
# install inferCNV for module 5.2
if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
BiocManager::install("infercnv")
```

2.2 Python packages

For module 4.2, we need one Python package scvelo. If you haven’t used Python before, we recommend installing it by using Anaconda, which contains Python 3.8 and various useful tools.

2.2.1 Installation on Windows

Go to Anaconda webpage; click ‘Download’ button to download Anaconda for Windows (with Python3.8).

Double click the downloaded file and install Anaconda following the instructions. (Note, this requires about 3G disk space)
Open Anaconda Powershell Prompt and then create an new conda environment with name sgcell by typing
```
conda create -n sgcell python=3.8
```
Still in the terminal, and activate the environment by typing
```
conda activate sgcell
```
Install scVelo in this conda environment by typing this command in the shell:
```
pip install scvelo==0.2.2
```

You have successfully set up the base environment of conda and installed the scVelo tool in this environment.

2.2.2 Installation on macOS

In macOS, you could install Anaconda either in graphical mode or command line mode.

Option 1: installation in Graphical Mode (recommended)

This mode is very similar to Installation on Windows.

Go to Anaconda webpage; click ‘Get Additional Installers’ button and then select the 64-Bit Graphical Installer for MacOS.

Install Anaconda following the instructions.
Open Terminal (you can type in Spotlight Search) and then create an new conda environment with name sgcell by typing
```
conda create -n sgcell python=3.8
```
Still in the terminal, and activate the environment by typing
```
conda activate sgcell
```
Install scVelo in this conda environment by typing this command in the shell:
```
pip install scvelo==0.2.2
```

Option 2: installation in Command Line Mode

This mode is very similar to Installation on Linux.

Open macOS Terminal
Download Anaconda installer with wget https://repo.anaconda.com/archive/Anaconda3-2021.05-MacOSX-x86_64.sh
Install Anaconda with bash Anaconda3-2021.05-MacOSX-x86_64.sh; follow the prompts on the installer screens.

When you are asked Do you wish the installer to initialize Anaconda3 by running conda init, we recommend “yes.”
Close and then re-open your Shell, to make the changes take effect.
Create an new conda environment with name sgcell by typing
```
conda create -n sgcell python=3.8
```
Still in the terminal, and activate the environment by typing
```
conda activate sgcell
```
Install scVelo in this conda environment by typing this command in the shell:
```
pip install scvelo==0.2.2
```

2.2.3 Installation on Linux

Open Linux Shell.
Download Anaconda installer with wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
Install Anaconda with bash Anaconda3-2021.05-Linux-x86_64.sh; follow the prompts on the installer screens.

When you are asked Do you wish the installer to initialize Anaconda3 by running conda init, we recommend “yes.”
Close and then re-open your Shell, to make the changes take effect.
Create an new conda environment with name sgcell by typing
```
conda create -n sgcell python=3.8
```
Still in the terminal, and activate the environment by typing
```
conda activate sgcell
```
Install scVelo in this conda environment by typing this command in the shell:
```
pip install scvelo==0.2.2
```
Type conda list in Shell.
A list of installed packages appears if it has been installed correctly.