GWAS workshop

How to GWAS

There are two ways to work in the workshop:

• run Jupyter Notebook locally (highly recommended) or
• use an executable environment by clicking the Binder badge above.

For the first option, follow the instruction below:

Before the start..

Install conda

Check if conda is installed:

conda --version

When conda is not installed locally, we advise installing miniconda or anaconda.
Click here for more information on conda environments.

Create a conda environment, aka "Magic Box," to keep projects separate

Each environment can have its own set of packages and dependencies, which means that different projects can have different versions of libraries (and even Python itself) without interference. You can set up the environment for gwas-workshop by entering this in the command line:

conda env create -f environment.yml

and then activate the environment in a new bash window:

conda activate gwas

If creating takes too long and/or doesn't work, try step-by-step script:

./create_env.sh

Start

To use the notebooks locally, run in the command line from the working directory:

jupyter notebook

Be sure, that both R and python kernels are properly installed

To check this you need to click "New" at the left top side of the jupiter-page and be sure that you can create two types of netebooks:

• python
• R

Create new notebooks of each type, in the opened window write x = 0 in the first cell and click "Run".

If R kernel doesn't work,

• uninstall it from the command line jupyter kernelspec uninstall ir
• follow the instruction.

End

To leave the invoronment please run:

conda deactivate