doc/index.md: converted and updated from doc/index.org

doc/index.md

+
+## Vidjil – Documentation
+*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)*
+
+**[Vidjil](http://www.vidjil.org) is an open-source platform for the analysis of high-throughput
+sequencing data from lymphocytes.** [V(D)J recombinations](http://en.wikipedia.org/wiki/V\(D\)J_recombination) in lymphocytes are
+essential for immunological diversity. They are also useful markers of
+pathologies, and in leukemia, are used to quantify the minimal residual
+disease during patient follow-up. High-throughput sequencing (NGS/HTS) now
+enables the deep sequencing of a lymphoid population with dedicated [Rep-Seq](http://omictools.com/rep-seq-c424-p1.html)
+methods and software.
+
+### Web application, user documentation
+
+  - Tutorial "Mastering the Vidjil web application": [english](./tutorial/mastering-vidjil.html) ([pdf](./tutorial/mastering-vidjil.pdf)), [français](./tutorial/mastering-vidjil-fr.html)
+    ([pdf](./tutorial/mastering-vidjil-fr.pdf)). Start by this tutorial to have an overview of Vidjil.
+  - Web application [user manual](user.md)
+  - [Demo access](http://app.vidjil.org/) to the patient, experiment and sample server
+  - [Public datasets](http://www.vidjil.org/data/) supporting Vidjil publications
+
+### Algorithm, web application, server, developper documentation
+
+  - [Vidjil-algo documentation](vidjil-algo.md)
+  - [Encoding clones with V(D)J recombinations](vidjil-format.md), specification of the `.vidjil` file format
+  - [Server documentation](./server.html)
+
+These documentations and additional developer and maintainer documentation
+are availaible from the [doc/](http://gitlab.vidjil.org/tree/master/doc) directory in the source files.
+
+### Further help
+
+Further help can always be asked to <contact@vidjil.org>. We can also arrange
+phone or video meeting.

doc/index.org

-#+TITLE: Vidjil -- Documentation
-#+AUTHOR: The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Ryan and Tatiana)
-#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org-mode.css" />
-
-[[http://www.vidjil.org][Vidjil]] is an open-source platform for the analysis of high-throughput
-sequencing data from lymphocytes.  [[http://en.wikipedia.org/wiki/V(D)J_recombination][V(D)J recombinations]] in lymphocytes are
-essential for immunological diversity. They are also useful markers of
-pathologies, and in leukemia, are used to quantify the minimal residual
-disease during patient follow-up. High-throughput sequencing (NGS/HTS) now
-enables the deep sequencing of a lymphoid population with dedicated [[http://omictools.com/rep-seq-c424-p1.html][Rep-Seq]]
-methods and software.
-
-** Web application, user documentation
-   :PROPERTIES:
-   :CUSTOM_ID: web-application-user-documentation
-   :END:
-
--  Tutorial "Mastering the Vidjil web application": [[./tutorial/mastering-vidjil.html][english]] ([[./tutorial/mastering-vidjil.pdf][pdf]]), [[./tutorial/mastering-vidjil-fr.html][français]]
-  ([[./tutorial/mastering-vidjil-fr.pdf][pdf]]). Start by this tutorial to have an overview of Vidjil.
--  Web application [[./user.html][user manual]]
--  [[http://app.vidjil.org/][Demo access]] to the patient, experiment and sample server
--  [[http://www.vidjil.org/data/][Public datasets]] supporting Vidjil publications
-
-** Algorithm, web application, server, developper documentation
-   :PROPERTIES:
-   :CUSTOM_ID: algorithm-web-application-server-developper-documentation
-   :END:
-
--  [[./algo.html][Algorithm documentation]]
--  [[./format-analysis.html][Encoding clones with V(D)J recombinations]], specification of the .json file format
--  [[./server.html][Server documentation]]
-
-These documentations and additional developer and maintainer documentation
-are availaible from the [[https://git.vidjil.org/tree/master/doc][doc/]] directory in the source files.
-** Further help
-   :PROPERTIES:
-   :CUSTOM_ID: further-help
-   :END:
-
-Further help can always be asked to [[mailto:contact@vidjil.org][contact@vidjil.org]]. We can also arrange
-phone or Skype meeting.

mkdocs.yml

@@ -8,6 +8,7 @@ repo_url: https://gitlab.inria.fr/vidjil/vidjil
 repo_name: gitlab
 
 pages:
+    - / : index.md
     - web platform, user manual: user.md
     - locus and recombinations: locus.md
     - vidjil-algo: vidjil-algo.md