https://github.com/hammerlab/wobidisco
Workflows Bioinformatics and Discoballs: The Biokepiverse
https://github.com/hammerlab/wobidisco
Last synced: 8 months ago
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Workflows Bioinformatics and Discoballs: The Biokepiverse
- Host: GitHub
- URL: https://github.com/hammerlab/wobidisco
- Owner: hammerlab
- Created: 2017-08-02T15:10:47.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2017-09-19T20:20:09.000Z (over 8 years ago)
- Last Synced: 2025-10-08T22:43:22.820Z (8 months ago)
- Size: 19.5 KB
- Stars: 5
- Watchers: 8
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
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README
Wobidisco
=========
This is the umbrella documentation/tooling project for:
- [Biokepi](https://github.com/hammerlab/biokepi): a library of composable
“pieces of bioinformatics workflows” (a.k.a. *“nodes”*).
- [Ketrew](https://github.com/hammerlab/ketrew): a computational workflow
manager on which Biokepi is based.
- [Coclobas](https://github.com/hammerlab/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](https://github.com/hammerlab/epidisco): a Biokepi workflow used in
production for a clinical trial; i.e. an actively maintained large workflow
example.
- [Secotrec](https://github.com/hammerlab/secotrec): a deployment/administration
tool for Ketrew/Coclobas setups.
Documentation
-------------
Individual projects have detailed documentation websites at
.
The following tutorials are available here:
- [Running](./doc/running-local.md) 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](./doc/debug-workflow-node.md) a “debug” workflow node to
experiment/troubleshoot commands within the same environment as the one of the
workflow (Secotrec-based).
- [Generating](./doc/biokepi-input-scripts.md)
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](https://travis-ci.org/hammerlab/wobidisco)).
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