:orphan:

.. _install:

************
Installation
************

Dependancies
############

External software dependancies
------------------------------

Macapype relies heavily on other neuroimaging Softwares, predominentyly:

* `FSL <http://www.fmrib.ox.ac.uk/fsl/index.html>`_
* `ANTS <http://stnava.github.io/ANTs/>`_
* `AFNI <https://afni.nimh.nih.gov/>`_
* `SPM <https://www.fil.ion.ucl.ac.uk/spm/>`_

for frioul users, here is what should be added at the end of your .bash_personal
 in /home/nom.p (only accessible from a node, i.e once you have type frioul_interactive)

.. code-block:: bash

    export PATH=$PATH:/hpc/soft/afni/afni/
    export ANTSPATH=/hpc/soft/ANTS/antsbin/bin
    export PATH=$ANTSPATH:$PATH
    export PATH=$PATH:/hpc/soft/ANTS/ANTs/Scripts/
    #FSLDIR=/hpc/soft/fsl/fsl_5.0.10/
    FSLDIR=/hpc/soft/fsl/fsl_6.0.1/
    #FSLDIR=/hpc/soft/fsl/fsl_5.0.11/
    . ${FSLDIR}/etc/fslconf/fsl.sh
    PATH=${FSLDIR}/bin:${PATH}
    export FSLDIR PATH
    FSLOUTPUTTYPE=NIFTI_GZ
    export FSLOUTPUTTYPE

Python packages dependancies
----------------------------

Macapype relies on python packages. Here we provide installations using Anaconda

Creating environment with all packages
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In case you have access to a conda environment, here is the procedure to initialize your own environnment (called "macapype", but can be called the name you prefer):

.. code-block:: bash

    $ conda init bash
    $ conda create -n macapype_env python=3.7
    $ conda activate macapype_env

Install macapype package
########################

from github
-----------

.. _git_install:

Using git
~~~~~~~~~

.. code:: bash

    $ git clone https://github.com/Macatools/macapype.git
    $ cd macapype
    $ python setup.py develop --user

Using pip
~~~~~~~~~

.. code:: bash

    $ pip install git+https://github.com/Macatools/macapype

.. _pip_install:

from pypi
---------

Macapype is available on * `pypi.org <https://pypi.org/project/macapype/>`_:

If 'pip' package is installed on your system, you can install the lastest stable version with:

.. code:: bash

    $ pip install macapype


From conda
-----------

Macapype is also available on `Anaconda cloud <https://anaconda.org/macatools/macapype>`_:

If 'conda' (Anaconda, or miniconda) is installed on your system, you can type:

.. code:: bash

    $ conda install -c macatools macapype

!!!! The lastest version of macapype (0.2.1) is not available, due to the inclusion of packages that are not yet packaged in conda
use "pip install macapype" or "git clone https://github.com/Macatools/macapype.git" till further notice

Testing the install
###################


.. code:: bash

    $ ipython

.. code:: ipython

    In [1]: import macapype