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# Pulling Bio.Tools (API) content to generate HTML pages
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## Building the Docker image
First build the docker image based on a fresh ubuntu 14 and a clear conda environment. 
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```
docker build -t biotools-api . 
```
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## Running the Docker image
Then run a container based on this image, it activates the conda environment and launches a jupyter notebook. The command line ends with an URL to connect to the jupyter notebook. Finally you cna execute the different cells to interact with the bio.tools API and produce an HTML representation. 
```
docker run -p 8888:8888 -i -t biotools-api
```

## Automation
The jupyter notebook can be launched as a regular python script : 
```
jupyter nbconvert --to notebook --inplace --execute biotools-notebook.ipynb 
```
This is done through the Gitlab continuous integration framework (CI) : https://gitlab.univ-nantes.fr/bird_pipeline_registry/html-tools-catalog/pipelines. A file `out.html` is generated each night and after each commit. This file is commited and pushed to this git repository and can be accessed here : https://gitlab.univ-nantes.fr/bird_pipeline_registry/html-tools-catalog/raw/master/out.html