Commit 2614654b by Eric Coissac

Change the install documentation

parent 6bfec50f
......@@ -20,7 +20,7 @@ Ecology Resources*, submitted.
:latex:`\vspace{\fill}`
Installing the ``OBITools``
---------------------------
===========================
Availability of the ``OBITools``
................................
......@@ -57,11 +57,11 @@ application not installed by default. The Python included in the system is not
suitable for running the ``OBITools``. You have to install a complete distribution
of Python that you can download as a `MacOSX package from the Python website <https://www.python.org/downloads/>`_.
User level installation
.......................
Downloading and installing the ``OBITools``
...........................................
There is two main ways for installing the ``OBITools``. The easiest one is to install them
using the :download:`get-obitools.py <../../../get_obitools/get-obitools.py>` script.
The ``OBITools`` are downloaded and installed using the :download:`get-obitools.py <../../../get_obitools/get-obitools.py>` script.
This is a user level installation that does not need administrator privilege.
Once downloaded, move the file :download:`get-obitools.py <../../../get_obitools/get-obitools.py>` in the directory where you want to install
the ``OBITools``. From a Unix terminal you must now run the command :
......@@ -98,44 +98,15 @@ Once activated you can desactivate the ``OBITools`` byt typing the command ``exi
System level installation
.........................
As all the Python software deposited on `PyPI <https://pypi.python.org/pypi/obitools>`_, ``OBITools`` can be
installed using the `pip` (`https://pypi.python.org/pypi/pip <https://pypi.python.org/pypi/pip>`_) command.
We recommand to use `pip` over `easy_install` as python package manager.
If you have not ``pip`` installed on your computer, please visite the
following page: `http://pip.readthedocs.org/en/latest/installing.html <http://pip.readthedocs.org/en/latest/installing.html>`_ .
Remember that Python 2.7, and a C compiler have to be installed before the ``OBITools``.
To install ``OBITools`` you have first to install dependencies
.. code-block:: bash
> pip install -U virtualenv
> pip install -U sphinx
> pip install -U cython
You can now install ``OBITools`` themselves.
.. code-block:: bash
> pip install -U obitools
Perhaps that on your system, the system administrator privilege are required to realise
these installations. If you are yourself administrator of your computer run the above commands
with the ``sudo`` command in front.
.. code-block:: bash
> sudo pip install -U virtualenv
> sudo pip install -U sphinx
> sudo pip install -U cython
> sudo pip install -U obitools
To install the ``OBITools`` at the system level you can follow two options :
- copy the ``obitools`` script in a usual directory for installing program like ``/usr/local/bin``
but never move the ``OBITools`` directory itself after the installation by the
:download:`get-obitools.py <../../../get_obitools/get-obitools.py>`.
- The other solution is to add the ``export/bin`` directory located in the ``OBITools`` directory
to the ``PATH``environment variable.
Retrieving the sources of the OBITools
......................................
......@@ -169,16 +140,14 @@ From the directory where you retrieved the sources, execute the following comman
> cd OBITools
> python setup.py build
> python setup.py install
> python setup.py --serenity install
Once installed, you can test your installation by running the commands of the
:doc:`tutorials <./tutorials>`.
Introduction
------------
============
DNA metabarcoding is an emerging approach for biodiversity studies (Taberlet et
al. 2012). Originally mainly developed by microbiologists (e.g. Sogin et al.
......@@ -303,7 +272,7 @@ plant taxonomic and growth form diversity. Molecular Ecology, 21, 3647-3655.
Basic concepts of the ``OBITools``
----------------------------------
==================================
Once installed, the ``OBITools`` enrich the Unix command line interface with a set
of new commands dedicated to NGS data processing. Most of them have a name
......
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