# ok, API

Official branch (master)

To help people maximize the extensibility and automation capability of Seven Bridges products, we're happy to share example API code. ok, API contains examples have been used to address common user wants and needs. They are divided into recipes & tutorials.

• "How do I do this one thing?" You want a recipe, which is a modular example of common operations.
• "How do I complete my entire analysis?" You want a tutorial, which may combine multiple recipes to go from start to finish of an analysis.

The recipe and tutorial folders in this repository are subdivided into CGC (the Cancer Genomics Cloud) and SBPLAT (the Seven Bridges Platform). This separation ensures we link to the appropriate docs. Switching environments is as easy as changing

# [USER INPUT] specify platform {cgc, sbpla}
prof = 'cgc'

to

# [USER INPUT] specify platform {cgc, sbpla}
prof = 'sbpla'

in the second code cell of any recipe (Note some features are available on one platform but not the other). Each folder has it's own readme files within each folder which details the scripts. Feedback and improvements are welcome.

Background

This repository covers the Seven Bridges Plaform and the Cancer Genomics Cloud. To learn more, see their documentation.

• The Seven Bridges Platform documentation is at docs.sevenbridges.com. In particular, see the API documentation.
• The Cancer Genomics Cloud documentation is at docs.cancergenomicscloud.com. In particular, see the API documentation.

Branches

Note there are two branches of this repository. You are on the master branch. We are currently populating this branch.

• master: This was released April 2016 and uses sevenbridges-python, the official Seven Bridges Python bindings. This branch includes most of the API functionality and is compatible with Python 2.6+ and 3.
• advanced_access: This was developed from January to May 2016 and uses apimethods.py. This is an unofficial branch where we may roll out new features. Currently there are more notebooks here. It is only compatible with Python 2.7.

Notes

0. We ask that you limit parallel tasks to 200 at a time¹. If you need to run more, that is great, but please get in touch with us so we don't run out of cloud.
1. This is compatible with Python 2.6+ and Python 3.
2. This is an beta and we are constantly working on improving our examples. Expect the awesomeness to continue.
3. Please share your feedback on our CGC forum or by emailing [email protected].
4. We are happy to recieve Pull Requests with your improvements or Issues which we will fix asap.

¹ This limit is a rule of thumb for the CGC, it also depends on the complexity of the workflow and input files. For Seven Bridges Platform users, this limit depends on your contract.

Good luck, have fun!