01-Prerequisites.Rmd

# Prerequisites {#env-pre}

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.

## R packages

1. For module 4.2, we need `reticulate` to import the Python package (see 
[next section](#python_packages). You can install it within R:

    ```
    # install reticulate for module 4.2
    install.packages("reticulate")
    ```

2. For module 5.1, we need `cardelino`, which is only available at 
[GitHub](https://github.com/single-cell-genetics/cardelino), 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)
    ```

3. 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/
<br/>
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")
    ```

## Python packages {#python_packages}
For module 4.2, we need one Python package [scvelo](https://scvelo.readthedocs.io/).
If you haven't used Python before, we recommend installing it by using [Anaconda](https://docs.anaconda.com/anaconda/), which contains Python 3.8 and 
various useful tools.

### Installation on Windows {#conda_install_windows}

1. Go to [Anaconda](https://www.anaconda.com/products/individual) webpage; click 'Download' button to download Anaconda for Windows (with Python3.8).

```{r conda_fig1, echo=FALSE, message=FALSE, warning=FALSE, fig.align="center", out.width='65%'}
knitr::include_graphics("./images/conda_download_installer1.png")
```

2. Double click the downloaded file and install Anaconda following the instructions. (Note, this requires about 3G disk space)

3. Open `Anaconda Powershell Prompt` and then create an new conda environment 
with name `sgcell` by typing

    ```
    conda create -n sgcell python=3.8
    ```
    
4. Still in the terminal, and activate the environment by typing

    ```
    conda activate sgcell
    ```

5. Install `scVelo` in this conda environment by typing this command in the shell:
   ```
   pip install scvelo==0.2.2
   ```

```{r conda_fig2, echo=FALSE, message=FALSE, warning=FALSE, fig.align="center", out.width='65%'}
knitr::include_graphics("./images/conda_scvelo.png")
```

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



### Installation on macOS {#conda_install_mac}

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](#conda_install_windows).

1. Go to [Anaconda](https://www.anaconda.com/products/individual) webpage; click 'Get Additional Installers' button and then
   select the `64-Bit Graphical Installer` for MacOS.

```{r conda_fig3, echo=FALSE, message=FALSE, warning=FALSE, fig.align="center", out.width='65%'}
knitr::include_graphics("./images/conda_download_installer2.png")
```

2. Install Anaconda following the instructions.

3. 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
    ```
    
4. Still in the terminal, and activate the environment by typing

    ```
    conda activate sgcell
    ```

5. 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](#conda_install_linux).

1. Open macOS Terminal

2. Download Anaconda installer with `wget https://repo.anaconda.com/archive/Anaconda3-2021.05-MacOSX-x86_64.sh`

3. Install Anaconda with `bash Anaconda3-2021.05-MacOSX-x86_64.sh`; follow the prompts on the installer screens.  
<br/>
When you are asked `Do you wish the installer to initialize Anaconda3 by running conda init`, we recommend "yes".

4. Close and then re-open your Shell, to make the changes take effect.

5. Create an new conda environment with name `sgcell` by typing

    ```
    conda create -n sgcell python=3.8
    ```
    
6. Still in the terminal, and activate the environment by typing

    ```
    conda activate sgcell
    ```

7. Install `scVelo` in this conda environment by typing this command in the shell:
   ```
   pip install scvelo==0.2.2
   ```


### Installation on Linux {#conda_install_linux}

1. Open Linux Shell.

2. Download Anaconda installer with `wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh`

3. Install Anaconda with `bash Anaconda3-2021.05-Linux-x86_64.sh`; follow the prompts on the installer screens.  
<br/>
When you are asked `Do you wish the installer to initialize Anaconda3 by running conda init`, we recommend "yes".

4. Close and then re-open your Shell, to make the changes take effect.

5. Create an new conda environment with name `sgcell` by typing

    ```
    conda create -n sgcell python=3.8
    ```
    
6. Still in the terminal, and activate the environment by typing

    ```
    conda activate sgcell
    ```

7. Install `scVelo` in this conda environment by typing this command in the shell:
   ```
   pip install scvelo==0.2.2
   ```

6. Type `conda list` in Shell. 
<br/>
A list of installed packages appears if it has been installed correctly.