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Pre-course

Preparation for the workshop

This workshop will comprise both lectures and hands-on exercises. While you will be able to follow all exercises from the html files, we recommend that you prepare by:

 

Programming with R and Python

The course will be taught using both R and Python depending on the tools available. While you will be able to follow all lectures and exercises conceptually, it is helpful if you are familiar with basic usage of both programming languages:

You should also be familiar with basic command line input ( mkdir , cd, ls, cp, mv).

 

Installing and setting up Docker

To reproduce all analyses you will need to Install Docker Links to an external site. . Afterwards, you will have to Download the Github repository with all notebooks,  Create the containers, Launch rstudio or jupyter, and Stop the containers.

Download the Github repository

Download and unzip the github repository from here Links to an external site..

Alternatively run:
wget -qO- https://github.com/NBISweden/workshop_omics_integration/archive/refs/heads/main.zip | bsdtar -xvf-;
mv workshop_omics_integration-main workshop_omics_integration

Note that you download it manually you should name the unziped folder as workshop_omics_integration. All the subsequent commands should be run in the parent of this directory.

Create the containers

At this point you need to create the two containers for all Rstudio or Jupyter notebooks. In a directory containing the unzip folder  workshop_omics_integration, create the containers by either:

Download image from Dockerhub (recommended)

Pull and start the images. Remember to replace <yourpassword> with your password, and /path/to/your/  with the path to your directory. If you want to use the current working directory, use $(pwd) in MacOS/Linux and ${PWD} in Windows powershell. In Windows 10, you can run the command below without sudo.

  ########### Rstudio image ###########   
  # Your user is 'omics' (without the quotes)
  sudo docker run -d --rm -p 8787:8787 \
    -e PASSWORD=<yourpassword> \
    -v /path/to/your/workshop_omics_integration:/home/omics/workshop_omics_integration/ \
    ruibenfeitas/rstudio:30_08_2021



  ########### Jupyter image ###########
  # Your user is 'jovyan' (without the quotes)
  # Replace <yourpassword> with your desired password
  sudo docker run -d --rm -p 8888:8888 \
  -e JUPYTER_TOKEN=<yourpassword> \
  -v /path/to/your/workshop_omics_integration/:/home/jovyan/workshop_omics_integration/ \
  ruibenfeitas/jupyter:30_08_2021

Your username for Rstudio will be omics your password will be omics. For jupyter, your password will be omics.

Download the dockerfiles from github

On github you will find the dockerfiles necessary from the github repository, under workshop_omics_integration/docker/  (you need the files Dockerfile_jupyter, Dockerfile_rstudio, docker-compose.yml and environment_jupyter), Install docker compose Links to an external site. and then:

## copy the dockerfiles found in the downloaded directory to the directory above
cp -r /path/to/your/workshop_omics_integration/docker/*  /path/to/your/

Build and start the containers with:

docker-compose up -d --build

Your username for Rstudio will be omics your password will be omics. For jupyter, your password will be omics.

Launch RStudio or Jupyter

Ensure you have followed all the instructions above and that your containers are running. If you have followed the instructions from the recommended solution you can simply access either RStudio or Jupyter from your browser with:

localhost:8888 to launch jupyter

localhost:8787 to launch rstudio

All notebooks are found within the folder workshop_omics_integration/  . If you want to verify that your containers are running use docker ps .

Stop the containers

To stop the containers write docker stop [container name]