README.md

Session 2: Federated Analysis - Find and access data in the cloud via Data Connect and Data Repository Service (DRS)

Outline

Time: Sunday, July 10th, 2022 @ 12 pm - 1 pm

Slides: link

Participants will use python clients for GA4GH services and write scripts in Jupyter notebooks.

Participants will interact with Driver Project implementations of Data Connect and DRS to locate and access files in datasets such as TCGA, GTEx, and TopMed and run workflows against them using WES (though that could be the add in the following session).

Tutorial

Open a terminal in your chosen python3 environment

Session specific requirements

If you are using Python virtual environments and set one up for the tutorial activate that environment now.

Install Jupyter

pip install jupyter

Install fasp-clients

• Install the fasp-clients branch of fasp-scripts. FASP is the GA4GH Federated Analysis Systems Project.

pip install git+https://github.com/ga4gh/fasp-clients

Clone or pull the respository for this tutorial

git pull https://github.com/ga4gh/ismb-2022-ga4gh-tutorial

Cloud credits

Starter accounts with cloud credits on selected platforms (to be listed e.g. Seven Bridges Cancer Genomics Cloud)

Create a project in the Cancer Genomics Cloud

Open http://cgc.sbgenomics.com and login with your username and password.

From the Projects menu select Create a Project

Fill in project details

Obtain an authentication token and save it to disk

Go to the Developer Menu and copy the authentication token to the clipboard

Open the file

ismb-2022-ga4gh-tutorial/sessions/session2/keys/sbcgc_key.json

Replace your_token_here with the token copied from the page above.

{"auth_token" : "your_token_here"}

Create a folder in your home directory called .keys

Copy the sbcgc_key.json file there.

mkdir ~/.keys
cd sessions
cp session2/keys/sbcgc_key.json ~/.keys

Note: you may save the file elsewhere. If so, make a note of the location you saved it to as you will need to replace the default path later.

python ismb_test/test_sbcgc_auth.py ~/.keys/sbcgc_key.json

Start Jupyter

cd ../sessions
jupyter notebook

Click on session1 to open the folder

Click on 1-1 Access token check.ipynb

Follow the instructions in the notebook

Check for a successful response

Close the browser tab or window to return to the notebook

Click on the .. folder icon to navigate back up to the sessions folder.

Click on session2 and open the 2-1 Basic DRS.ipynb notebook.

Work through the exercises in the notebook.