Name: wobidisco
Owner: Hammer Lab
Description: Workflows Bioinformatics and Discoballs: The Biokepiverse
Created: 2017-08-02 15:10:47.0
Updated: 2017-11-20 05:27:42.0
Pushed: 2017-09-19 20:20:09.0
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README
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
