https://github.com/soedinglab/bamm-suite

De-novo motif discovery and optimization
https://github.com/soedinglab/bamm-suite

bamm bioinformatics

Last synced: 11 months ago
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De-novo motif discovery and optimization

• Host: GitHub
• URL: https://github.com/soedinglab/bamm-suite
• Owner: soedinglab
• License: gpl-3.0
• Created: 2017-02-11T09:51:02.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2019-11-27T10:30:17.000Z (over 6 years ago)
• Last Synced: 2025-01-09T06:51:24.933Z (over 1 year ago)
• Topics: bamm, bioinformatics
• Language: Python
• Homepage:
• Size: 880 KB
• Stars: 3
• Watchers: 8
• Forks: 1
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
# About BaMM-suite

[![License](https://img.shields.io/github/license/soedinglab/bamm-suite.svg)](https://choosealicense.com/licenses/gpl-3.0/)

[![Issues](https://img.shields.io/github/issues/soedinglab/bamm-suite.svg)](https://github.com/soedinglab/bamm-suite/issues)

BaMM-suite is the motif finding suite developed by the Soedinglab.

This repository is the entry point to the BaMM universe. Here you can find documentation, common functionality and helper scripts and a clean interface into the BaMM world.

# Dependencies

## Build dependencies

- cmake

- python >= 3.3

## Building the documentation

- sphinx

- sphinx-argparse

- sphinx_rtd_theme

- sphinxcontrib-autoprogram

# Installing

## Cloning the repository

```bash

   git clone https://github.com/soedinglab/bamm-suite.git

```

## Python package

BaMM-suite is a python package and can be installed with pip.

```bash

    cd bamm-suite

    pip install bamm-suite-py

```

## Helper scripts

To install all helper scripts into `/user/bin`, you would do:

```bash

   mkdir build_cmake && cd build_cmake

   cmake -DCMAKE_INSTALL_PREFIX:PATH=/user ..

   make install

```

# Building the documentation

An html version of the documentation can be built by running following commands from the root of the repository.

    cd docs

    make html

# Usage of the commandline tools

BaMM-suite installs the command line script `bamm`. Run `bamm --help` for a list of available submodules.

# License

BaMM-suite is licensed under the [GNU General Public License v3.0](https://choosealicense.com/licenses/gpl-3.0/).