Installation¶

You can install RAPIDS using Docker (the fastest), or native instructions for MacOS and Linux (Ubuntu). Windows is supported through Docker or WSL.

Docker

Install Docker

Pull our RAPIDS container

docker pull moshiresearch/rapids:latest

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 moshiresearch/rapids:latest
```
Pull the latest version of RAPIDS
```
git pull
```
Make RAPIDS script executable
```
chmod +x rapids
```
Check that RAPIDS is working
```
./rapids -j1
```
Optional. You can edit RAPIDS files with vim but we recommend using Visual Studio Code and its Remote Containers extension
How to configure the Remote Containers extension
- Make sure RAPIDS Docker container is running
- Install VS Code and its Remote - Containers extension
- Click the Remote Explorer icon on the left-hand sidebar (the icon is a computer monitor)
- On the top right dropdown menu, choose Containers
- Right-click on the moshiresearch/rapids container in the CONTAINERS tree and select Attach to Container. A new VS Code window should open
- In the new window, open the /rapids/ folder via the File/Open... menu
- Run RAPIDS inside a terminal in VS Code. Open one with the Terminal/New Terminal menu

Warning

If you installed RAPIDS using Docker for Windows on Windows 10, the container will have limits on the amount of RAM it can use. If you find that RAPIDS crashes due to running out of memory, increase this limit.

MacOS

We tested these instructions in Catalina and Big Sur

M1 Macs

RAPIDS can run on M1 Macs, the only changes as of Feb 21, 2021 are:

R needs to be installed via brew under Rosetta (x86 arch) due to incompatibility issues with some R libraries. To do this, run your terminal via Rosetta, then proceed with the usual brew installation command. Use x86 brew to install R and restore RAPIDS’ packages (snakemake -j1 renv_install & snakemake -j1 renv_restore).
There is a bug related to timezone codes. We set the correct TZ_DIR in renv/activate.R (line #19) Sys.setenv("TZDIR" = file.path(R.home(), "share", "zoneinfo")) (RAPIDS does this automatically).

Install brew

Install MySQL

brew install mysql
brew services start mysql

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")'

Install miniconda (restart your terminal afterwards)

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

Clone our repo

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

Create a python virtual environment

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

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.
Make RAPIDS script executable
```
chmod +x rapids
```
Check that RAPIDS is working
```
./rapids -j1
```

Ubuntu

We tested RAPIDS on Ubuntu 18.04 & 20.04. Note that the necessary Python and R packages are available in other Linux distributions, so if you decide to give it a try, let us know and we can update these docs.

Install dependencies

sudo apt install libcurl4-openssl-dev
sudo apt install libssl-dev
sudo apt install libxml2-dev
sudo apt install libglpk40

Install MySQL

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

Add key for R’s repository.

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

Add R’s repository

Ubuntu 18.04 Bionic

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

Ubuntu 20.04 Focal

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

Install R 4.0. If you have other instances of R, we recommend uninstalling them
```
sudo apt update
sudo apt install r-base
```

Install Pandoc and rmarkdown

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

Install git
```
sudo apt install git
```
Install miniconda
Restart your current shell

Clone our repo:

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

Create a python virtual environment:

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

Install the R virtual environment management package (renv)
```
snakemake -j1 renv_install
```
Restore the R virtual environment
Ubuntu 18.04 Bionic (fast)
Run the following command to restore the R virtual environment using RSPM binaries
```
R -e 'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))'
```
Ubuntu 20.04 Focal (fast)
Run the following command to restore the R virtual environment using RSPM binaries
```
R -e 'renv::restore(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))'
```
Ubuntu (slow)
If the fast installation command failed for some reason, you can restore the R virtual environment from source:
```
R -e '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.
Make RAPIDS script executable
```
chmod +x rapids
```
Check that RAPIDS is working
```
./rapids -j1
```

Windows

There are several options varying in complexity:

You can use our Docker instructions (tested)
You can use our Ubuntu 20.04 instructions on WSL2 (not tested but it will likely work)
Native installation (experimental). If you would like to contribute to RAPIDS you could try to install MySQL, miniconda, Python, and R 4.0+ in Windows and restore the Python and R virtual environments using steps 6 and 7 of the instructions for Mac. You can get in touch if you would like to discuss this with the team.