DNAnexus General Background

Some Miscellaneous Information about the DNAnexus Platform

Job Execution Overview

There are three types of executable on the platform:

  1. Applets – non optimized programs (not fully vetted by DNAnexus) these are either home-grown or provide on the platform.
  2. Apps – DNAnexus deployed applications that have been optimized and vetted.
  3. Workflows – collections of Apps or Applets strung together to perform a complex set of operations.

Job Flow:

Additionally, there are VISUALIZERS that are combinations of html and javascript (do not spawn on a worker node) used for data visualization… these can set up to reference files on the platform.


Data Transfer Methods (All are checked for integrity by MD5SUM check ??)

  • Upload/Download via the Web pages
  • Upload via the dx-upload tool
  • Upload via the incremental upload tool (for “live data” direct from sequencers)

Note: Globus is also supported… details to be forthcoming.


Controls on Job Execution (Safety valves)

  • All jobs have a preset max number of nodes (~100).
  • Jobs that run more than 24 hours generate warning emails.
  • All apps have (should have) reasonable timeout policies.