README.md

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# Met4J : the Java library for metabolic networks

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**Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.**


Met4j is composed by three main modules:
- [met4j-core](met4j-core/README.md): it's the key module which contains all the core 
classes for handling metabolic networks
- [met4j-io](met4j-io/README.md): for importing/exporting metabolic networks in several 
formats (SBML, KEGG, TSV)
- [met4j-graph](met4j-graph/README.md): for performing graph-based topological analysis of metabolic networks.  

The package [met4j-toolbox](met4j-toolbox/README.md) contains high-level apps that can be run in command line by using either jar file or Singularity or Docker containers.


## Installation

### From Maven

Install all modules :  
```
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-toolbox</artifactId>
<version>1.4.0</version>
</dependency>
```

or a specific module (example : met4j-core ):  
```
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-core</artifactId>
<version>1.4.0</version>
</dependency>
```

### From Source

```
git clone https://forgemia.inra.fr/metexplore/met4j.git;
cd met4j;
mvn clean install 
```

Read [met4j-toolbox](met4j-toolbox/README.md) to see how to get jar, Docker or Singularity packages containing all the met4-toolbox apps.

## Usage

User documentation for the library modules can be found in each module's own README.  
Detailed code examples can be found at [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).
Javadoc can be found at [https://javadoc.io/doc/fr.inrae.toulouse.metexplore](https://javadoc.io/doc/fr.inrae.toulouse.metexplore)

## Contributing

Pull requests are welcome **on the gitlab repo** ([https://forgemia.inra.fr/metexplore/met4j](https://forgemia.inra.fr/metexplore/met4j)). For major changes, please open an issue first to discuss what you would like to change.  

Please make sure to update tests as appropriate.  

## Issues

Issues or suggestions can be posted [here](https://github.com/MetExplore/met4j/issues).

## License

Met4J is distributed under the open license [CeCILL-2.1](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html) (compatible GNU-GPL).