Commit ccd2e284 by Eric Coissac

Prepare version 1.0.000

@tweet:Preparing the OBITools 1.00 final version
parent d223a879
......@@ -36,6 +36,11 @@ html:
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The e-Pub pages are in $(BUILDDIR)/epub."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
......
......@@ -237,3 +237,10 @@ class CustomLatexFormatter(LatexFormatter):
PygmentsBridge.latex_formatter = CustomLatexFormatter
#--option for epub format ----------------------------------
epub_publisher=u"metabarcoding.org"
epub_author=u"OBITools Development Team"
......@@ -22,18 +22,35 @@ Ecology Resources*, submitted.
Installing the ``OBITools``
---------------------------
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
have to be installed prior to the ``OBITools``.
Prerequisites
.............
To install and test the ``OBITools``, you need several softwares to be installed on your
To install the ``OBITools``, you need that these softwares are installed on your
system:
* Python 2.7 (installed by default on most ``Unix`` systems, available from
`the Python website <http://www.python.org/>`_)
* Cython (available from the `Cython website <http://http://cython.org/>`_)
* ``gcc`` and ``gmake`` (installed by default on most ``Unix`` systems, available from the
* ``gcc`` (installed by default on most ``Unix`` systems, available from the
GNU sites dedicated to `GCC <https://www.gnu.org/software/gcc/>`_ and
`GMake <https://www.gnu.org/software/make/>`_)
If you want to compile by yourself the ``OBITools``, you will need to install futhermore:
* Cython (available from the `Cython website <http://http://cython.org/>`_)
* any subversion client (a list of clients is avalaible from
`Wikipedia <http://en.wikipedia.org/wiki/Comparison_of_Subversion_clients>`_)
......@@ -296,19 +313,6 @@ the ``OBITools`` library are developed using `cython` (http://cython.org/, a Pyt
to C compiler) or the C language directly. The ``OBITools`` compile on Unix systems
including Linux and MacOSX.
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). All the sources
can be downloaded from our subversion server
(http://www.grenoble.prabi.fr/public-svn/OBISofts/obitools). The ``OBITools`` are
deposited on the Python package index (https://pypi.python.org/pypi/obitools)
and therefore can be installed using the classical python package installers
`pip` (https://pypi.python.org/pypi/pip) or `easy\_install`
(https://pypi.python.org/pypi/setuptools). Python 2.7, a C compiler and `cython`
have to be installed prior to the ``OBITools``.
References
..........
......@@ -328,8 +332,8 @@ Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E (2011) ecoPrimers:
inference of new DNA barcode markers from whole genome sequence analysis.
Nucleic Acids Research, 39, e145.
.. |Pipeline example for a standard biodiversity survey| image:: fig-Pipeline.pdf
.. |Pipeline example for a standard biodiversity survey| image:: fig-Pipeline.*
.. |The structure of an OBITools sequence record and its representation in fasta and fastq formats| image:: fig-Record.pdf
.. |The structure of an OBITools sequence record and its representation in fasta and fastq formats| image:: fig-Record.*
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