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. ...@@ -21,10 +21,11 @@ list of PDB files.
Be sure to check if the following packages are correctly installed with Be sure to check if the following packages are correctly installed with
your python installation or virtual environment. your python installation or virtual environment.
- **pip** (>= 9.0) - **pip** (>= 18.0)
- **setuptools** (>= 18.0) - **git** (>= 2.0)
- **cns-solve** (1.21) - **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 : 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 : ...@@ -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 For more information about installation and usage, please refer to the
[ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec) [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 ## Contributing
......
...@@ -8,20 +8,11 @@ ...@@ -8,20 +8,11 @@
usage usage
contributing contributing
.. toctree::
:maxdepth: 4
:caption: API
Core package <api/aria.core>
Conbox package <api/aria.conbox>
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
:caption: Tutorial :caption: Tutorial
tutorial/setup tutorial
tutorial/run
tutorial/analysis
.. toctree:: .. toctree::
:maxdepth: 2 :maxdepth: 2
...@@ -29,3 +20,11 @@ ...@@ -29,3 +20,11 @@
examples/bpt1/bpt1 examples/bpt1/bpt1
examples/malecoli/malecoli 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 : ...@@ -203,8 +203,8 @@ version 1.2 :
2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define 2. Edit the file ``cns_solve_env`` in the directory ``cns_solve_1.1`` to define
the location of the CNSsolve directory. the location of the CNSsolve directory.
3. Go to directory ``cns_solve_1.1`` and type ``make install``. This should start 3. Go to the directory ``cns_solve_1.1`` and type ``make install``. This should
the compilation process. start the compilation process.
.. Footnotes .. 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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