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Project Structure

Table of Contents

  1. Overview
  2. Installation and Management Utilities
  3. Frameworks
  4. Tool Suites
  5. Command Line Utility
  6. Documentation
  7. Public Server Support
  8. Singularity Container Support
  9. End User Assistance

Overview

The MDI codebase is organized into modular GitHub repositories that provide ease and flexibility for end users and developers. They separate functions to allow users to access – and developers to work on – the tools most relevant to them.

The following diagram illustrates the overall project structure.

Installation and Management Utilities

The MDI Manager is an R package that provides commands to install() pipelines and apps and run() the web interface. The concept is similar to the BiocManager utility of the Bioconductor project.

The MDI Installer is a wrapper that makes it easier to run the manager utility. It also provides a streamlined, non-R installation for people who will only use Stage 1 pipelines on an HPC server, skipping the slower installation of Stage 2 R Shiny apps when they aren’t needed.

Even better and easier to use is the MDI Desktop App, an Electron app that helps users connect to HPC servers via SSH and to install and run both Stage 1 Pipelines and Stage 2 Apps, all from a convenient desktop program. The Desktop is usually the best way access MDI tools, whether locally or remotely.

These are the repositories for the MDI installation and management utilities:

Frameworks

The MDI framework repositories help run Stage 1 Pipelines and Stage 2 Apps by providing code and functions that are common and useful across many tools. They are the foundational building blocks that make it easy to quickly develop new tools. As illustrated above, there are two separate frameworks, one for Stage 1 pipelines and one for Stage 2 apps.

The pipelines and apps frameworks are maintained by the MDI as open-source projects that you are invited to help improve. These are the repositories for the frameworks:

Most users will simply install the frameworks using the installer or desktop app and not think about them further.

Tool Suites

The code that does the specific work of a pipeline or app is found in a tool suite repository. Tools suites are developed by anyone, such as a core facility, research laboratory, or funded project. We encourage you to make your suite repositories public as open-source code, which makes it easy to publish work performed with them. However, you can develop and use private suites if you provide a token that allows access to the repositories.

A suite, i.e., repository, might hold only one pipeline or app, but we encourage you to combine related tools into a single suite as makes sense for your activities. For example, a research laboratory might combine its machine learning tools into a single suite. Creating suites also makes it easy to share modular code between tools.

We provide mechanisms for you to register your suite with the MDI and will engage in a basic review to ensure that your code is well-constructed, appropriate, and not nefarious.

It is easy to build your own tool suites using the following template repository, emulating the demo tool suite derived from it:

Command Line Utility

Once a user has installed the MDI, they can run Stage 1 Pipelines using the ‘mdi’ command line utility. This single wrapper utility provides a unified method of executing and monitoring pipelines. It is one of the many advantages of adding your pipeline to an MDI suite.

In remote usage modes, Stage 1 Pipelines can also be run in the web interface’s Pipeline Runner app, which calls ‘mdi’ on your behalf.

Documentation

The MDI helps developers maintain robust, standardized documentation for all project-associated code using GitHub features including README.md files and GitHub Pages. The following are the repositories for this documentation site, our basic training tutorials, and the MDI Jekyll documentation themes and templates. The latter are also built into the suite template, above.

Public Server Support

The MDI runs equally well on many computer infrastructures. The following repositories help you quickly create a publicly addressable MDI server installation using Amazon Web Services (AWS).

Singularity Container Support

The MDI project places a premium on controlled compute environments using conda as well as Singularity containers. We maintain AWS machine images that help developers quickly build their own tool containers for sharing with others.

End User Assistance

The recommended method for describing data to be analyzed and other options for Stage 1 pipelines is to write YAML-format data scripts, a.k.a. job configuration files. A final simple template repository helps end users organize collections of data scripts in their own git repositories and archive them using GitHub.