Commit aa673927 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Updated README.rst and installation doc

parent 2f0f4437
......@@ -12,6 +12,10 @@ de Novo Ambiguous Restraints for Iterative Assignment
:target: https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master
:alt: Coverage report
.. image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtl589-blue.svg
:target: https://doi.org/10.1093/bioinformatics/btl589
:alt: DOI status
``ariaec`` is a Python_ library that provides *de novo* structure prediction
based on ARIA_ pipeline and evolutionary restraints inferred from co-evolution.
......@@ -38,8 +42,15 @@ your python installation or virtual environment.
3. Extract the files and run ``pip install .`` inside the new directory
More explanation about the ``pip`` installation can be found in the
:doc: `installation` section
For more information about installation and usage, please refer to the
`ARIAEC documentation<http://bis-aria.pages.pasteur.fr/ariaec>`_.
Contributing
------------
Please read `guidelines for contributing <CONTRIBUTING.md>`_ for any
suggestions or bug report.
.. Hyperlinks
......
......@@ -54,12 +54,12 @@ shift
ARGS=${@}
case ${CMD} in
maptools )
ec )
exec /usr/bin/ariaec ${ARGS} ;;
main )
exec /usr/bin/aria2 ${ARGS} ;;
* )
echo "command \"${CMD}\" is not supported. available commands: \"maptools\"|\"main\""
echo "command \"${CMD}\" is not supported. available commands: \"ec\"|\"main\""
exit 127
;;
esac
......
......@@ -3,7 +3,19 @@ Installation
.. warning::
Installation procedure may change in the future
Installation procedure may change in the future especially after the
transition to Python 3 which should be the next major update.
Download
--------
ZIP_ or TAR_ version can be downloaded from Gitlab_ website.
.. code-block:: bash
wget -O ariaec-master.tar.gz https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.tar.gz
mkdir ariaec-master && tar xzf ariaec-master.tar.gz -C ariaec-master --strip-components 1
Dependencies
------------
......@@ -13,25 +25,37 @@ below are actually correctly installed in your environment.
* ``pip`` (>= 9.0)
* ``setuptools`` (>= 18.0)
* ``numpy`` (>= 1.11)
* ``matplotlib``
Basic installation
------------------
The recommended installation process is to use up to date ``pip`` commands with
the last ``ariaec`` version. For the moment, the packages used Python 2.7 but
the transition to Python 3 is planned in the near future.
.. note::
Pip install may lead to unexpected computation time if your directory
contains more than the ARIA package. In most cases, this is due to
virtualenv folders within the same directory. In those situations,
``pip install .`` will also look into virtualenvs folders. A simple
``pip install --user .`` will also look into virtualenvs folders. A simple
workaround to solve this issue is to create a empty folder for the
installation as described below.
.. code-block:: bash
cd ariaec-master
mkdir build_aria && cp -r aria setup.py PKG-INFO build_aria/
cd build_aria
pip install --user .
Singularity
-----------
Dockerfile
----------
......@@ -40,4 +64,10 @@ using the ``Dockerfile`` in the ``aria`` directory [1]_.
.. Footnotes
.. [1] In order to build it, you have to be root on your computer.
\ No newline at end of file
.. [1] In order to build it, you have to be root on your computer.
.. Hyperlinks
.. _ZIP: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.zip
.. _TAR: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.tar
.. _Gitlab: https://gitlab.pasteur.fr/bis-aria/ariaec
\ No newline at end of file
Command Line Interface
======================
The command line interface is accessible by calling ``ariaec`` (or ``ec2aria``
for older versions) within the terminal at the end of the installation process.
Two CLI:abbr:`Command Line Interface` are accessible after the installation.
* :command:`aria2`: interface for setting up and running an ARIA project
* :command:`ariaec` [1]_: interface for converting and analyze contact maps
ARIA2
-----
Please refer to the `ARIA documentation <http://aria.pasteur.fr/>`_ for more
explanations.
ARIAEC
------
.. code-block:: bash
......@@ -59,7 +70,7 @@ for older versions) within the terminal at the end of the installation process.
Setup
--------------
+++++
Translate contact maps as distance restraints and setup ARIA infrastructure.
.. code-block:: bash
......@@ -118,39 +129,43 @@ Translate contact maps as distance restraints and setup ARIA infrastructure.
Bbconv
--------------
++++++
Translate BBcontacts as distance restraints which can be used during
`setup <Setup_>`_.
Maplot
--------------
++++++
Contactmap analysis and visualisation tool.
Analysis
--------------
++++++++
Analyze results from an ARIA project.
PDBQual
--------------
+++++++
Call PDB quality tools.
TBL2XML
--------------
+++++++
Convert TBL restraints in ARIA XML format.
PDBDist
--------------
+++++++
Extract distance from a culled list of PDBs.
PDBStat
--------------
+++++++
Statistical analysis of ``pdbdist`` results.
IniConv
--------------
+++++++
Convert a INI file as csv for easy readability.
.. Hyperlinks
.. [1] :command:`ec2aria` for older versions
\ No newline at end of file
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