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.. _install:
======================
Download and install
======================
This page covers the necessary steps to install Nipype.
Download
--------
Release 0.5.2: [`zip <http://github.com/nipy/nipype/zipball/0.5.2>`_ `tar
<http://github.com/nipy/nipype/tarball/0.5.2>`_]
Development: [`zip <http://github.com/nipy/nipype/zipball/master>`_ `tar
<http://github.com/nipy/nipype/tarball/master>`_]
`Prior downloads <http://github.com/nipy/nipype/tags>`_
To check out the latest development version::
git clone git://github.com/nipy/nipype.git
Install
-------
The installation process is similar to other Python packages.
If you already have a Python environment setup that has the dependencies listed
below, you can do::
easy_install nipype
or::
pip install nipype
Debian and Ubuntu
~~~~~~~~~~~~~~~~~
Add the `NeuroDebian <http://neuro.debian.org>`_ repository and install
the ``python-nipype`` package using ``apt-get`` or your favourite package
manager.
Mac OS X
~~~~~~~~
The easiest way to get nipype running on MacOSX is to install EPD_ and then add
nibabel and nipype by executing::
easy_install nibabel
easy_install nipype
If you are running a 64 bit version of EPD, you will need to compile
ETS. Instructions for a 64-bit boot mode are available:
https://gist.github.com/845545
From source
~~~~~~~~~~~
If you downloaded the source distribution named something
like ``nipype-x.y.tar.gz``, then unpack the tarball, change into the
``nipype-x.y`` directory and install nipype using::
python setup.py install
**Note:** Depending on permissions you may need to use ``sudo``.
Testing the install
-------------------
The best way to test the install is to run the test suite. If you have
nose_ installed, then do the following::
python -c "import nipype; nipype.test()"
you can also test with nosetests::
nosetests --with-doctest /software/nipy-repo/masternipype/nipype
--exclude=external --exclude=testing
All tests should pass (unless you're missing a dependency). If SUBJECTS_DIR
variable is not set some FreeSurfer related tests will fail. If any tests
fail, please report them on our `bug tracker
<http://github.com/nipy/nipype/issues>`_.
On Debian systems, set the following environment variable before running
tests::
export MATLABCMD=$pathtomatlabdir/bin/$platform/MATLAB
where, $pathtomatlabdir is the path to your matlab installation and
$platform is the directory referring to x86 or x64 installations
(typically glnxa64 on 64-bit installations).
Avoiding any MATLAB calls from testing
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On unix systems, set an empty environment variable::
export NIPYPE_NO_MATLAB=
This will skip any tests that require matlab.
Dependencies
------------
Below is a list of required dependencies, along with additional software
recommendations.
Must Have
~~~~~~~~~
Python_ 2.6 -2.7
Nibabel_ 1.0
Neuroimaging file i/o library
NetworkX_ 1.0 - 1.4
Python package for working with complex networks.
NumPy_ 1.3 - 1.6
SciPy_ 0.7 - 0.10
Numpy and Scipy are high-level, optimized scientific computing libraries.
Enthought_ Traits_ 4.0.0
.. note::
Full distributions such as pythonxy_ or EPD_ provide the above packages,
except Nibabel_.
Strong Recommendations
~~~~~~~~~~~~~~~~~~~~~~
IPython_ 0.10.2 - 0.12
Interactive python environment. This is necessary for some parallel
components of the pipeline engine.
Matplotlib_ 1.0
Plotting library
Sphinx_
Required for building the documentation
`Graphviz <http://www.graphviz.org/>`_
Required for building the documentation
Interface Dependencies
~~~~~~~~~~~~~~~~~~~~~~
These are the software packages that nipype.interfaces wraps:
FSL_
4.1.0 or later
matlab_
2008a or later
SPM_
SPM5/8
FreeSurfer_
FreeSurfer version 4 and higher
AFNI_
2009_12_31_1431 or later
Slicer_
3.6 or later
Nipy_
0.1.2+20110404 or later
Nitime_
(optional)
Camino_
Camino2Trackvis_
ConnectomeViewer_
.. include:: ../links_names.txt
|
