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.
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).
JSON input descriptions for Biokepi workflows which use the
Biokepi_pipeline_edsl.Pipeline_library.Inputmodules (Epidisco is one of them).
Testing The Examples
tools/check-examples.sh (with the tool
run the examples in the Markdown files
(incl. with TravisCI).
You can run it by simply:
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