Update documentation front page

doc/index.rst

@@ -11,6 +11,38 @@ genomes based on *shared genomic regions* and *genomic contact data*.
 Currently, we use orthologous genes as shared regions and Hi-C data as contacts
 information. Thus, you must already have these data.
 
+
+License
+-------
+
+The source code is available `here`_ and is licensed under the CeCILL V2.1
+since it was written when I was working in a `CNRS`_ laboratory. The CeCILL
+license is close to the GNU GPL and compatible with it. The full text for
+the license is available in the `LICENSE file in the repository`_.
+
+
+Citing
+------
+
+PhyloHiC has been written during my PhD thesis work, and is described in the
+third chapter of `my thesis`_ (in French). Moreover, the results presented
+there come from the pipeline documented here. Thus, if you use this pipeline,
+please cite my thesis:
+
+::
+
+    Sylvain Pulicani.
+    Lien entre les réarrangements chromosomiques et la structure de la chromatine chez la Drosophile.
+    Autre [cs.OH]. Université Montpellier, 2018. Français.
+    NNT: 2018MONTS105
+    HAL: tel-02161932
+
+Please note that a scientific publication is coming.
+
+
+-------------------------------------------------------------------------------
+
+
 This documentation is divided in three sections:
 
 .. toctree::
@@ -23,7 +55,8 @@ This documentation is divided in three sections:
    scripts_and_api
    file_formats
 
-..
-   1. Introduction to the ideas and the general process
-   2. Actually running an analysis
-   3. Scripts and API documentation
+
+.. _my thesis: https://tel.archives-ouvertes.fr/tel-02161932
+.. _here: https://gite.lirmm.fr/pulicani/phyloHiC
+.. _CNRS: https://www.cnrs.fr/en
+.. _LICENSE file in the repository: https://gite.lirmm.fr/pulicani/phyloHiC/blob/master/LICENSE