Welcome to the Lakitu developer documentation!¶
The Lakitu project is a computational infrastructure built to run mass spectrometry data processing pipelines on the cloud. A “pipeline” is a series of computational processing steps applied to an input data set (e.g. .raw files) to generate a desired result (e.g. a Skyline document). The project currently consists of the following components:
- AWS Infrastructure
- Cloudformation scripts to build a scalable compute environment on the Amazon cloud which is used to execute pipeline components (source).
- Dockerized Applications
- The software for each step of a processing pipeline is stored in a Docker container. (source, dockerhub).
- Local Command Line Client
- A local command line client which can be used to list available pipelines (from a pipeline index) and run them on the cloud infrastructure. Files are synced between the local system and Amazon S3 (source).
- Lakitu API
- An python interface which must be implemented by each Lakitu pipeline and Lakitu pipeline executor to coordinate exchange of information about the location and credentials needed for accessing AWS infrastructure (source).
- DIA Library Query Pipeline
- An example pipeline written to query DIA data using a spectral library (source).
Using this documentation¶
I highly recommended reading the Overview to get an idea of the structure of the entire project. Next, if you do not already have access to a working lakitu environment, you will want to check out the tutorial on creating the environment in Tutorials. If your goal is to do development work on any of the components, I recommend checking out the documentation for the specific component of interest.