Commit 62e288e4 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

docs: move tutorial section

parent d04bbc49
......@@ -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
......
......@@ -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>
......@@ -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
......
========
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
============
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