docs: move tutorial section

README.md

@@ -21,10 +21,11 @@ list of PDB files.
 Be sure to check if the following packages are correctly installed with
 your python installation or virtual environment.
 
-- **pip** (>= 9.0)
-- **setuptools** (>= 18.0)
+- **pip** (>= 18.0)
+- **git** (>= 2.0)
 - **cns-solve** (1.21)
-- **pbxplore** (>= 1.3.8)
+- **ccpnmr analysis** (optional)
+- **ccpn data model** (optional)
 
 Then the easiest solution is to call the **pip** command below :
 
@@ -33,7 +34,8 @@ Then the easiest solution is to call the **pip** command below :
 For more information about installation and usage, please refer to the
 [ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec)
 
-**ARIA contains patches for CNS-solve which needs to be compiled after the installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
+**ARIA contains patches for CNS-solve which needs to be compiled after the
+installation. Please follow [post installation instructions](http://bis-aria.pages.pasteur.fr/ariaec/installation.html#post-installation-instructions).**
 
     
 ## Contributing

docs/contents.rst

@@ -8,20 +8,11 @@
    usage
    contributing
 
-.. toctree::
-   :maxdepth: 4
-   :caption: API
-
-   Core package <api/aria.core>
-   Conbox package <api/aria.conbox>
-
 .. toctree::
    :maxdepth: 2
    :caption: Tutorial
 
-   tutorial/setup
-   tutorial/run
-   tutorial/analysis
+   tutorial
 
 .. toctree::
    :maxdepth: 2
@@ -29,3 +20,11 @@
 
    examples/bpt1/bpt1
    examples/malecoli/malecoli
+
+.. toctree::
+   :maxdepth: 4
+   :caption: API
+
+   Core package <api/aria.core>
+   Conbox package <api/aria.conbox>
+

docs/installation.rst

@@ -203,8 +203,8 @@ version 1.2 :
 2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define
 the location of the CNSsolve directory.
 
-3. Go to directory ``cns_solve_1.1`` and type ``make install``. This should start
-the compilation process.
+3. Go to the directory ``cns_solve_1.1`` and type ``make install``. This should
+start the compilation process.
 
 
 .. Footnotes

docs/tutorial.rst

+========
+Tutorial
+========
+
+Project preparation
+===================
+
+The ``ariaec`` Command Line Interface (CLI) is the main tool for
+converting and analyze contact map information. The main command of this
+interface is ``ariaec setup`` which create an ARIA project XML file. Then we can
+follow the usual steps for an ARIA project.
+
+Configuration file
+------------------
+
+All the parameters for ``ariaec`` commands are encapsulated on a configuration file in INI format
+
+
+Project template
+----------------
+
+
+Setup
+-----
+
+
+Running ARIA
+============
+