GSI is a team of bioinformaticians, software developers, and clinical genome interpreters at Ontario Institute for Cancer Research that develop, maintain, and operate the core analysis infrastructure, analyze genomic data produced at the institute, and support collaborators, researchers, and clinical trials with their bioinformatics analysis.

To support these activities, we have developed a large suite of open-source software that can be found under our Github organizations: oicr-gsi and miso-lims.

This repository is for some of the public documentation related to our clinical offerings.

These docs are built with Python 3 and Sphinx. It's best to install and run within a python virtual environment.

To install:

python3 -m pip install -r requirements.txt

To build:

make html

Open the local copy of the website at build/html/index.html

Documentation is written in reStructuredText. Here's a primer.

There's a python script that will automatically update the assay specific .csv files in source/sops/software according to the .txt files that are in the same directory.

1. Modify the list of workflows for the assay at source/sops/software.
2. Run make update.

• This command will download gsi_workflows.json from OICR, which is produced by https://github.com/oicr-gsi/workflowTracker/blob/main/workflow_tracker.py. You need to be on the VPN and have SSH keys set up for this to work.
• if you have a passphrase on your ssh key, it will ask you for it
• it will then use the list of workflows for each assay, pull out the appropriate clinical workflow information, and stick it in a csv file in source/sops/software

3. Commit the txt and generated csv files.

You can then use the csv in RST using the .. csv-table:: command.

Documentation pushed to the main branch is automatically built on RtD.

• Project page on RtD : https://app.readthedocs.org/projects/oicr-gsi/
• Latest documentation : https://oicr-gsi.readthedocs.io/en/latest/

Contact us either through the Github issue tracker on any project.