Bioinformatics Ketrew Pipelines
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
opam
src
tools
.gitignore
.travis.yml
LICENSE
Makefile
README.md
myocamlbuild.ml

README.md

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.