https://github.com/hammerlab/biokepi

Bioinformatics Ketrew Pipelines
https://github.com/hammerlab/biokepi

bioinformatics-ketrew-pipelines bioinformatics-pipeline ketrew ocaml

Last synced: 3 months ago
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Bioinformatics Ketrew Pipelines

• Host: GitHub
• URL: https://github.com/hammerlab/biokepi
• Owner: hammerlab
• License: apache-2.0
• Created: 2014-12-16T19:19:07.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2021-11-14T12:54:57.000Z (about 3 years ago)
• Last Synced: 2023-08-13T00:21:59.095Z (over 1 year ago)
• Topics: bioinformatics-ketrew-pipelines, bioinformatics-pipeline, ketrew, ocaml
• Language: OCaml
• Size: 1.87 MB
• Stars: 28
• Watchers: 9
• Forks: 4
• Open Issues: 86
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
Biokepi: Bioinformatics Ketrew Pipelines

========================================

This project provides a family of libraries to construct

“[Ketrew](https://github.com/hammerlab/ketrew/) Workflows” for

bioinformatics pipelines.

This should be considered *“alpha / preview”* software.

See the documentation at 

[`www.hammerlab.org/docs/biokepi/master`](http://www.hammerlab.org/docs/biokepi/master/index.html).

Build

-----

The main dependency is

[Ketrew](http://hammerlab.org/docs/ketrew/master/index.html) (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](src/doc/Use_the_demo.md).