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# Biohackathon 2019: Rare disease maps

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Code and comments to [https://r3.pages.uni.lu/biocuration/resources/biohackathon2019/rdmaps/](https://r3.pages.uni.lu/biocuration/resources/biohackathon2019/rdmaps/).

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#### Requirements

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- Java Runtime
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- Python 3.x
- R
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- zip utility
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Python needs to have packages decribed in `associations/requirement.txt` which can be installed
via

```commandline
pip3 install -r associations/requirement.txt
```

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If the pipeline is run at clean Linux installation you might need to install the following libraries 
(`sudo apt-get install` on Ubuntu) prior to running the code:
- libcurl
- libssl-dev
- libxml2-dev

### Execution

To execute the pipeline, set the values of parameters in the `PARAMETERS TO SET` 
section of the `assamble.sh` script file. The main parameter here is the list of
[Orphanet](https://www.orpha.net/consor/cgi-bin/index.php?lng=EN) disease numbers.
When the parameters are set, run the pipeline:

```
bash assemble.sh 
```

This will run the pipeline described in the next section and eventually output a
ZIP file with a map which can then be imported in [MINERVA](https://minerva.pages.uni.lu/doc/)
as a disease maps integrating all the found enriched pathways together with
genetic an variant [overlays](https://minerva.pages.uni.lu/doc/user_manual/v14.0/index/#overlays-tab).

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### Pipeline
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1. [Retrieval of gene-disease mappging and variants](associations/README.md).
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2. [Enrichment](enrichment/README.md)