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Pre-course

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Preparation for the tutorial

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 1. familiarizing yourself with basic R and Python, 2. installing the containers, and 3. going through the following 3 notebooks. If you want to run them in your system please see the labs page for setup instructions.

If you are interested you can go through the additional reading materials.

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).

Docker instructions

To reproduce all analyses you will need to:

If you have previously followed the conda instructions, we still recommend that you follow the instructions below as they may avoid some bugs.

Create the containers

At this point you need to create the two containers for all Rstudio or Jupyter notebooks. You can do so by choosing one of the following options:

**> Download image from Dockerhub** (recommended)

Pull and start the images

########### Rstudio image ###########
# Your user is 'omics' (without the quotes)
# Replace <yourpassword> with your desired password
sudo docker run -d --rm -p 8787:8787 -e PASSWORD=<yourpassword> ruibenfeitas/rstudio:16_07_2021

########### Rstudio image for meta analyses ###########
# Your user is 'omics' (without the quotes)
# Replace <yourpassword> with your desired password
sudo docker run -d --rm -p 8787:8787 -e PASSWORD=<yourpassword> ash706/omicsint_r

########### 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> ruibenfeitas/jupyter:16_07_2021
**> Download the dockerfiles from github**

On github you will find the dockerfiles necessary from the github repository. Download all files (Dockerfile_jupyter, Dockerfile_rstudio, docker-compose.yml and environment_jupyter), install docker compose and install git. Then:

## go to the dir where the dockerfiles are found
cd /path/to/dockerfiles

# clone into a subfolder `workshop`
git clone https://github.com/NBISweden/workshop_omicsint_ISMBECCB.git workshop

Build the containers

docker-compose build

At this point you can start and run the containers

########### Rstudio image ###########
# Your user is 'omics' (without the quotes)
# Replace <yourpassword> with your desired password
docker-compose up -d -p 8787:8787 -e PASSWORD=<yourpassword>

########### Jupyter image ###########
# Your user is 'jovyan' (without the quotes)
# Replace <yourpassword> with your desired password
docker-compose up -d -p 8888:8888 -e JUPYTER_TOKEN=<yourpassword>
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/ as indicated in the labs. 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].