Biokepi: Bioinformatics Ketrew Pipelines

This project provides a family of libraries to construct “Ketrew Workflows” for bioinformatics pipelines.

This should be considered “alpha / preview” software.

See the documentation at www.hammerlab.org/docs/biokepi/master.

Build

The main dependency is Ketrew (which requires OCaml ≥ 4.02.2).

To install the pre-release through opam:

opam pin add biokepi "https://github.com/hammerlab/biokepi.git#biokepi.0.0.0"
[opam install biokepi]

To use the master branch you need also to track the master branch of Ketrew:

opam pin add ketrew https://github.com/hammerlab/ketrew.git
opam pin add biokepi https://github.com/hammerlab/biokepi.git

To build locally:

make
make clean ; WITH_TESTS=true make  # To build also all the tests
make doc  # To build the documentation, then cf. _build/doc/index.html

Usage

The Biokepi module is the main entry point for most use cases.

There are “demo” command-line applications in the src/app/ directory and tests in src/test/.

The main demo application (src/app/main.ml) is documented here: Use the demo.