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# Map generator

This code assemble resources into a single map.

Piotr Gawron's avatar
Piotr Gawron committed
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## Description

The code is based on the [minerva source code](https://git-r3lab.uni.lu/minerva/core/tree/master). It downloads list of pathways provided as an input (from wikipathways or minerva instances) and merges them into single file. Additionally, data from text mining can be taken as an input and this information is incorporated into the whole map. Exported file is SBML file with layout, render and multi packages.

## License

GNU Affero General Public License v3.0

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## Requirements

* Java 8
* Maven 3.6

## Compilation

```
mvn -DskipTests=true clean install -pl biohackathon -am
```

The compiled runnable file will be located in biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar.

## Execution

To get information about parameters just run:

```
java -jar biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar
```

Sample usage:

```
java -jar biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file biohackathon/data/enrichr_output.txt --minerva-file  biohackathon/data/example_pathway_to_pull.txt --text-mining-file  biohackathon/data/brugada_output_file_omnipath.tsv --output-file output.xml
```