Installation

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

Docker

1. Install Docker

2. Pull our RAPIDS container

   docker pull agamk/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)

   docker run -it agamk/rapids:latest
   

4. Pull the latest version of RAPIDS

   git pull
   

5. Make RAPIDS script executable

   chmod +x rapids
   

6. Check that RAPIDS is working

   ./rapids -j1
   

7. Optional. You can edit RAPIDS files with vim but we recommend using Visual Studio Code and its Remote Containers extension

   How to configure Remote Containers extension

   • Make sure RAPIDS container is running
   • Install the Remote - Containers extension
   • Go to the Remote Explorer panel on the left hand sidebar
   • On the top right dropdown menu choose Containers
   • Double click on the agamk/rapids container in theCONTAINERS tree
   • A new VS Code session should open on RAPIDS main folder insidethe container.

MacOS

We tested these instructions in Catalina

1. Install brew

2. Install MySQL

   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

   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)

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

5. Clone our repo

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

6. Create a python virtual environment

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

7. Install R packages and virtual environment:

   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.

8. Make RAPIDS script executable

   chmod +x rapids
   

9. Check that RAPIDS is working

   ./rapids -j1
   

Ubuntu

We tested on Ubuntu 18.04 & 20.04

1. Install dependencies

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

2. Install MySQL

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

3. Add key for R’s repository.

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

4. Add R’s repository

   1. For 18.04
      

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

   2. For 20.04

      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

   sudo apt update
   sudo apt install r-base
   

6. Install Pandoc and rmarkdown

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

7. Install git

   sudo apt install git
   

8. Install miniconda

9. Restart your current shell

10. Clone our repo:

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

11. Create a python virtual environment:

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

12. Install R packages and virtual environment:

    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.

13. Make RAPIDS script executable

    chmod +x rapids
    

14. Check that RAPIDS is working

    ./rapids -j1