About the Rabix Suite
Overview
Rabix (Reproducible Analyses for Bioinformatics) is an open-source development kit from Seven Bridges for creating and running computational workflows in the Common Workflow Language (CWL) on your local machine.
The Rabix Suite consists of the Rabix Executor and the Rabix Composer. Use the Rabix Executor to execute and test CWL tools and workflows from the command line. Rabix Composer, which is powered by the Executor, provides an intuitive visual editor to view, edit, and run CWL tools and workflows from your desktop. Note that you can use Rabix Composer to create and edit CWL tools and workflows locally as well as use it to access and locally edit apps from supported cloud Platforms.
About the Common Workflow Language
The Common Workflow Language (CWL) is a specification for describing analysis tools and workflows in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing environments.
The Rabix suite supports both the older CWL version, sbg:draft-2, and the more recent CWL version, v1.0. CWL sbg:draft-2 includes extensions to CWL draft-2 that are specific to Seven Bridges. CWL v1.0 includes most of the Seven Bridges extensions from CWL sbg:draft-2 as part of the standard specification and is fully portable to other CWL v1.0-conformant executors.
Rabix Composer allows you to mix CWL 1.0 and CWL sbg:draft-2 components in the same workflow. Rabix Executor can execute these mixed workflows, but note that many other CWL executors don’t currently support mixed workflows.
Learn more about CWL in Rabix.
About tools, workflows, and apps
A tool is a CWL description of an individual command line utility and its options, inputs, and outputs. The CWL specification allows tools to be described in a standard and portable way.
Tools can be executed in isolation, or built into workflows, which are chains of one or more connected tools. Workflows can also contain other workflows. Workflows are also described in CWL.
Collectively, tools and workflows are often referred to as apps.
Supported cloud platforms
Seven Bridges maintains a series of cloud platforms which are compatible with the Rabix Suite. Use Rabix Composer to locally develop and test apps before pushing them to a platform. Or, access apps from platform projects to locally develop and test in Rabix Composer. See below for a list of supported platforms.
Seven Bridges Platform
The Seven Bridges Platform is a cloud-based environment for analyzing genomics data. It provides cloud-based access to public genomics reference files and datasets, and to public tools and workflows. You can also add your own data, tools and workflows and use them to build new workflows in combination with the publicly available tools and data.
The Seven Bridges Platform brings the power, efficiency and security of cloud infrastructure to your bioinformatics analyses. You can share your tools, data and results with your colleagues, and analyses are repeatable and reproducible.
CGC
The Cancer Genomics Cloud (CGC) offers similar functionality to the Seven Bridges Platform, but for academic users. It is funded by the National Cancer Institute, and includes The Cancer Genomics Atlas (TGCA) data.
If you do not have a Platform account, you can sign up for a free CGC account with a small amount of computational credit. You can connect your CGC account to Rabix Composer and use that to explore the Platform integration features.
Note that CGC accounts are intended for academic users. If you like what you see, and want to continue using the functionality on the CGC Platform for ongoing commercial purposes, you can contact Seven Bridges and discuss a paid-for account on The Seven Bridges Platform.
Cavatica
Cavatica also offers similar functionality to The Seven Bridges Platform, but is focussed on data analysis of pediatric cancers and rare diseases. It is accessible by licensed users only.