Use pre-built packages¶
Linux¶
We recommend that you use our repositories hosted at Open Build Service. We have build packages for most linux distributions. Visit this page to pick your distribution and follow instructions.
Note
moogli
(tool to visualize network activity) is not available for CentOS-6.
MacOSX¶
MacOSX support is not complete yet. The GUI does not work due to compatibility isses with PyQt package
available on homebrew See status of this ticket.
Python interface is available (latest version 3.1.2. Status)
and can be installed on MaxOSX using homebrew
$ brew install homebrew/science/moose
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 --depth 100
This will create folder called “moose” with source code. Or,
$ wget https://github.com/BhallaLab/moose/archive/master.zip
$ unzip master.zip
You can download other released versions from here.
Install dependencies¶
Depending on your operating system, names of following packages may vary.
Python interface for core MOOSE API (pymoose)¶
- Required
- Python For building the MOOSE Python bindings
- Python development headers and libraries, e.g. python-dev or python-devel
- NumPy ( >= 1.6.x) For array interface, e.g. python-numpy or numpy
- Optional
- NetworkX (1.x). Layout is of chemical models is computed using networkx.
- Matplotlib (>=1.1.x) For plotting simulation results
- python-libsbml For reading and writing chemical models in SBML format.
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 SUSE/OpenSUSE
$ sudo zypper install hdf5-devel cmake libgsl-dev python-devel python-numpy
build moose¶
$ cd /to/moose/source/code
$ mkdir _build
$ cd _build
$ cmake ..
$ make -j2 # using 2 core to build MOOSE
$ ctest --output-on-failure # optional
$ sudo make install
This will build 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.
>>> import moose
Graphical User Interface (GUI)¶
MOOSE-gui can be launched by running the following command
$ moosegui
Below are packages which you may need to install to be able to launch MOOSE Graphical User Interface.
- Required:
- PyQt4 (4.8.x)
On Ubuntu/Debian
, these can be installed with
$ sudo apt-get install python-qt4
On CentOS/Fedora/RHEL
$ sudo yum install python-qt4
Note
If you have installed moose
package, then GUI is launched by
running following commnad:
$ moosegui
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.
- Required
- OSG (3.2.x) For 3D rendering and simulation of neuronal models
- Qt4 (4.8.x) For C++ GUI of Moogli
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.