Workflows Bioinformatics and Discoballs: The Biokepiverse
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README.md

README.md

Wobidisco

This is the umbrella documentation/tooling project for:

  • Biokepi: a library of composable “pieces of bioinformatics workflows” (a.k.a. “nodes”).
  • Ketrew: a computational workflow manager on which Biokepi is based.
  • Coclobas: Ketrew can interact with Torque/PBS, Platform LSF, YARN, and other HPC schedulers; Coclobas is another such scheduler, specialized in cloud/docker computing environments (Google Container Engine, AWS Batch, or “local” Docker).
  • Epidisco: a Biokepi workflow used in production for a clinical trial; i.e. an actively maintained large workflow example.
  • Secotrec: a deployment/administration tool for Ketrew/Coclobas setups.

Documentation

Individual projects have detailed documentation websites at http://hammerlab.org/docs.

The following tutorials are available here:

  • Running Epidisco (or any Biokepi workflow) using Ketrew/Coclobas in local-docker mode (i.e. using Coclobas to schedule docker containers on a single machine).
  • Creating a “debug” workflow node to experiment/troubleshoot commands within the same environment as the one of the workflow (Secotrec-based).
  • Generating JSON input descriptions for Biokepi workflows which use the Biokepi_pipeline_edsl.Pipeline_library.Input modules (Epidisco is one of them).

Testing The Examples

We use tools/check-examples.sh (with the tool tools/code-of-markdown/) to run the examples in the Markdown files (incl. with TravisCI). You can run it by simply:

sh ./tools/check-examples.sh

if you are debugging, you may want to speed-up the script by not checking/installing the dependencies every time.

without_deps=true sh tools/check-examples.sh