master branchBiokepi is made of 5 libraries: 4 building blocs and 1 wrapping module
(Biokepi).
Biokepi contains a single module ./src/lib/biokepi.ml that wraps modules
from the other 4 libraries under a cleaner API.
Biokepi_run_environment (src/run_environment): is the common API used all
across the library (incl. extensions to Ketrew's EDSL, and the Machine.t
interface to computing infrastructure).
Biokepi_environment_setup: provides a set of (optional/customisable)
defaults to setup a Biokepi.Machine.t, it includes Ketrew workflow-nodes to
install tools (Machine.Tool.t) and to download/prepare reference data
(reference genomes, databases, etc.).
Biokepi_bfx_tools: contains the implementations of the Ketrew workflows to
run all supported bioinformatics tools.
Biokepi_pipeline_edsl: in-progress high-level API, to build very concise,
typed, and readable bioinformatics workflows.
There are “demo” command-line applications in the src/app directory and tests
in src/test/.