@@ -26,15 +26,11 @@ Availability of the ``OBITools``
................................
The ``OBITools`` are open source and protected by the CeCILL 2.1 license
(`http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html <http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html>`_). All the sources
can be downloaded from our subversion server
(`http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools <http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools>`_). The ``OBITools`` are
deposited on the Python package index (`https://pypi.python.org/pypi/obitools <https://pypi.python.org/pypi/obitools>`_)
and therefore the easiest way to install the ``OBITools`` is to use the python package installers
`pip` (`https://pypi.python.org/pypi/pip <https://pypi.python.org/pypi/pip>`_) that will take in charge the installation of the other
dependencies. 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>`_ . Python 2.7, and a C compiler
Once activated you can desactivate the ``OBITools`` byt typing the command ``exit``.
.. code-block:: bash
> exit
OBITools are no more activated, Bye...
======================================
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
Retrieving the sources of the OBITools
......................................
If you want to compile by yourself the ``OBITools``, you will need to install the same
prerequisite:
.. code-block:: bash
> pip install -U virtualenv
> pip install -U sphinx
> pip install -U cython
moreover you need to install any subversion client (a list of clients is available from `Wikipedia <http://en.wikipedia.org/wiki/Comparison_of_Subversion_clients>`_)
Then you can download the
.. code-block:: bash
> svn co http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools/trunk OBITools
> svn co http://www.grenoble.prabi.fr/public-svn/OBISofts/OBITools/branches/OBITools-1.00/ OBITools
This command will create a new directory called ``OBITools``.
Compiling and installing the Obitools
.....................................
Compiling and installing the ``OBITools``
.........................................
From the directory where you retrieved the sources, execute the following commands:
...
...
@@ -85,7 +182,7 @@ Introduction
DNA metabarcoding is an emerging approach for biodiversity studies (Taberlet et
al. 2012). Originally mainly developed by microbiologists (e.g. Sogin et al.
2006), it is now widely used for plants (e.g. Sønstebø et al. 2010, Parducci et
2006), it is now widely used for plants (e.g. Sonstebo et al. 2010, Parducci et
al. 2012, Yoccoz et al. 2012) and animals from meiofauna (e.g. Chariton et al.
2010, Baldwin et al. 2013) to larger organisms (e.g. Andersen et al. 2012,
Thomsen et al. 2012). Interestingly, this method is not limited to *sensu
...
...
@@ -131,7 +228,7 @@ records based on the taxonomy.
