rapids/docs/setup/installation.md

Installation

You can install RAPIDS using Docker (the fastest), or native instructions for MacOS and Ubuntu

=== "Docker"

1.  Install [Docker](https://docs.docker.com/desktop/)

2.  Pull our RAPIDS container
    ``` bash
    docker pull moshiresearch/rapids:latest`
    ```

3.  Run RAPIDS\' container (after this step is done you should see a
    prompt in the main RAPIDS folder with its python environment active)

    ``` bash
    docker run -it moshiresearch/rapids:latest
    ```

4.  Pull the latest version of RAPIDS

    ``` bash
    git pull
    ```

5. Make RAPIDS script executable
    ```bash
    chmod +x rapids
    ```

6.  Check that RAPIDS is working
    ``` bash
    ./rapids -j1
    ```
7.  *Optional*. You can edit RAPIDS files with `vim` but we recommend using `Visual Studio Code` and its `Remote Containers` extension

    ??? info "How to configure Remote Containers extension"

        - Make sure RAPIDS container is running
        - Install the [Remote - Containers extension](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers)
        - Go to the `Remote Explorer` panel on the left hand sidebar
        - On the top right dropdown menu choose `Containers`
        - Double click on the `moshiresearch/rapids` container in the`CONTAINERS` tree
        - A new VS Code session should open on RAPIDS main folder inside the container.

=== "MacOS" We tested these instructions in Catalina

1.  Install [brew](https://brew.sh/)

2.  Install MySQL

    ``` bash
    brew install mysql
    brew services start mysql
    ```

3.  Install R 4.0, pandoc and rmarkdown. If you have other instances of R, we recommend uninstalling them

    ``` bash
    brew install r
    brew install pandoc
    Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
    ```

4.  Install miniconda (restart your terminal afterwards)

    ``` bash
    brew cask install miniconda
    conda init zsh # (or conda init bash)
    ```

5.  Clone our repo

    ``` bash
    git clone https://github.com/carissalow/rapids
    ```

6.  Create a python virtual environment

    ``` bash
    cd rapids
    conda env create -f environment.yml -n rapids
    conda activate rapids
    ```

7.  Install R packages and virtual environment:

    ``` bash
    snakemake -j1 renv_install
    snakemake -j1 renv_restore
       
    ```

    !!! note
        This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.

5. Make RAPIDS script executable
    ```bash
    chmod +x rapids
    ```

8.  Check that RAPIDS is working
    ``` bash
    ./rapids -j1
    ```

=== "Ubuntu"

We tested on Ubuntu 18.04 & 20.04

1.  Install dependencies

    ``` bash
    sudo apt install libcurl4-openssl-dev
    sudo apt install libssl-dev
    sudo apt install libxml2-dev
    ```

2.  Install MySQL

    ``` bash
    sudo apt install libmysqlclient-dev
    sudo apt install mysql-server
    ```

3.  Add key for R's repository.

    ``` bash
    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
    ```

4. Add R's repository

    1. For 18.04    
    ``` bash
    sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/'
    ```

    1. For 20.04
    ``` bash
    sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
    ```

5. Install R 4.0. If you have other instances of R, we recommend uninstalling them

    ``` bash
    sudo apt update
    sudo apt install r-base
    ```

6.  Install Pandoc and rmarkdown

    ``` bash
    sudo apt install pandoc
    Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
    ```

7.  Install git

    ``` bash
    sudo apt install git
    ```

8.  Install [miniconda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html)

9.  Restart your current shell

10. Clone our repo:

    ``` bash
    git clone https://github.com/carissalow/rapids
    ```

11. Create a python virtual environment:

    ``` bash
    cd rapids
    conda env create -f environment.yml -n MY_ENV_NAME
    conda activate MY_ENV_NAME
    ```

7.  Install R packages and virtual environment:

    ``` bash
    snakemake -j1 renv_install
    snakemake -j1 renv_restore
       
    ```

    !!! note
        This step could take several minutes to complete, especially if you have less than 3Gb of RAM or packages need to be compiled from source. Please be patient and let it run until completion.

5. Make RAPIDS script executable
    ```bash
    chmod +x rapids
    ```

8.  Check that RAPIDS is working
    ``` bash
    ./rapids -j1
    ```