index.rst

Installation
============

Use pre-built packages
----------------------

Linux
^^^^^

We recommend that you use our repositories hosted at `Open Build Service
`_. We have packages for the following distributions

- Debian 7.0, 8.0
- Ubuntu 12.04, 14.04, 15.04, 15.10, 16.04
- CentOS 6, 7
- Fedora 20, 21, 22, 23
- OpenSUSE 13.1, 13.2, Factory ARM, Leap 42.1, Tumbleweed
- SLE 12, 12 SP1
- RHEL 7
- Scientific Linux 7

Visit `this page
`_
pick you distribution and follow instructions.

.. note::
``moogli`` (tool to visualize network activity) is not available for CentOS-6.

.. raw:: html

.. todo:: Packages for gentoo, Arch Linux

Mac OSX
^^^^^^

Download the ``dmg`` file from `here `_.

Alternatively, you can use ``homebrew`` to install ``moose``
::
$ brew install homebrew/science/moose

Windows/Cygwin
^^^^^^^^^^^^^^

Building MOOSE
--------------

In case your distribution is not listed on `our repository page
`_
, or if you want to build the lastest development code, read on.

First, you need to get the source code. You can use ``git`` (clone the
repository) or download snapshot of github repo by clicking on `this link
`_.::
$ git clone https://github.com/BhallaLab/moose

Or,
::
$ wget https://github.com/BhallaLab/moose/archive/master.zip
$ unzip master.zip

If you don't want lasest snapshot of ``MOOSE``, you can download other released
versions from here `https://github.com/BhallaLab/moose/releases`.

Install dependencies
~~~~~~~~~~~~~~~~~~~

Next, you need to install required dependencies. Depending on your OS, names of
following packages may vary.

- cmake (version 2.8 or higher)
- gsl-1.16 or higher `download `_.
- libhdf5 development package e.g. `libhdf5-serial-dev` or `libhdf5-devel`
- python development package e.g. `python-dev` or `python-devel`
- numpy e.g. `python-numpy` or `numpy`

Most of the dependencies can be installed using package manager.

On ``Debian/Ubuntu``
::
$ sudo apt-get install libhdf5-dev cmake libgsl0-dev libpython-dev python-numpy

.. note::
Ubuntu 12.04 does not have required version of ``gsl`` (required 1.16 or
higher, available 1.15). On Ubuntu 16.04, package name is ``libgsl-dev``.

On ``CentOS/Fedora/RHEL/Scientific Linux``
::
$ sudo yum install hdf5-devel cmake libgsl-dev python-devel python-numpy

On ``OpenSUSE``
::
$ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy

Now use `cmake` to build moose
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. codeblock:: bash
$ cd /to/moose/source/code
$ mkdir _build
$ cd _build
$ cmake ..
$ make
$ ctest --output-on-failure # optional

This will build pyMOOSE (MOOSE's python extention), `ctest` will run few tests to
check if build process was successful.

.. note::
To install MOOSE into non-standard directory, pass additional argument
`-DCMAKE_INSTALL_PREFIX=path/to/install/dir` to cmake
::
$ cmake -DCMAKE_INSTALL_PREFIC=$HOME/.local ..

To use different version of python
::
$ cmake -DPYTHON_EXECUTABLE=/opt/python3/bin/python3 ..

After that installation is pretty easy
::
$ sudo make install

If everything went fine, you should be able to import moose in python shell.

.. code-block:: python
import moose

Graphical User Interface (GUI)
------------------------------

You can get the source of ``moose-gui`` from `here
`_. You can download it either by
clicking on `this link `_
or by using ``git`` ::
$ git clone https://github.com/BhallaLab/moose-gui

To be able to launch ``moose-gui``, you need to install some more packages

- matplotlib
- python-qt4

On ``Ubuntu/Debian``, these can be installed with
::
$ sudo apt-get install python-matplotlib python-qt4

On ``CentOS/Fedora/RHEL``
::
$ sudo yum install python-matplotlib python-qt4

Now you can fire up the GUI
::
$ cd /to/moose-gui
$ python mgui.py

.. note::
If you have installed ``moose`` package, then GUI is launched by
running following commnad::
$ moose

Building moogli
---------------

``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
be found `here `_.

`Moogli` is part of `moose` package. Building moogli can be tricky because of
multiple depednecies it has.

To get the latest source code of ``moogli``, click on `this link `_.

Moogli depends on ``OpenSceneGraph`` (version 3.2.0 or higher) which may not
be easily available for your operating system.
For this reason, we distribute required ``OpenSceneGraph`` with ``moogli``
source code.

Depending on distribution of your operating system, you would need following
packages to be installed.

On ``Ubuntu/Debian``
::
$ sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev

On ``Fedora/CentOS/RHEL``
::
$ sudo yum install sip-devel PyQt4-devel qt4-devel libjpeg-devel PyQt4

On ``openSUSE``
::
$ sudo zypper install python-sip python-qt4-devel libqt4-devel python-qt4

After this, building and installing ``moogli`` should be as simple as
::
$ cd /path/to/moogli
$ mkdir _build
$ cd _build
$ cmake ..
$ make
$ sudo make install

If you run into troubles, please report it on our `github repository
`_.