INSTALL.md

Pre-built packages

Use our repositories hosted at Open Build Service. We have packages for Debian, Ubuntu, CentOS, Fedora, OpenSUSE/SUSE, RHEL, Scientific Linux. Visit the following page and follow the instructions there.

https://software.opensuse.org/download.html?project=home:moose&package=moose

Building from source

First, Download the latest source code of moose from github.

$ git clone https://github.com/BhallaLab/moose
$ cd moose

Install dependencies

For moose-core:

• gsl-1.16 or higher.

• libhdf5

• libsbml (optional)

  Make sure that libsml is installed with zlib and lxml support. If you are using buildtools, then use the following to install libsbml.

    - wget http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/stable/libSBML-5.9.0-core-src.tar.gz
    - tar -xzvf libSBML-5.9.0-core-src.tar.gz 
    - cd libsbml-5.9.0 
    - ./configure --prefix=/usr --with-zlib --with-bzip2 --with-libxml 
    - make 
    - ctest --output-on-failure # optional
    - sudo make install 

For python module of MOOSE, following additional packages are required:

• Development package of python e.g. libpython-dev
• python-numpy

For python-gui, we need some more addtional packages

• matplotlib
• setuptools (cmake uses it to install moose python extension and moogli)
• suds
• Python bindings for Qt4 or higher
• Python OpenGL
• Python bindings for Qt's OpenGL module

On Ubuntu-120.4 or higher, these can be installed with:

sudo apt-get install python-matplotlib python-qt4 python-qt4-gl 

Use cmake to build moose:

$ mkdir _build
$ cd _build 
$ cmake -DWITH_DOC=OFF ..
$ make 
$ ctest --output-on-failure

This will build moose and its python extentions, ctest will run few tests to check if build process was successful.

To install MOOSE into non-standard directory, pass additional argument -DCMAKE_INSTALL_PREFIX=path/to/install/dir to cmake.

After that installation is pretty easy.

Install

$ sudo make install

Building and installing moogli

MOOGLI is subproject of moogli for visualizing models. Details can be found here.

MOOGLI dependencies are huge! It uses OpenSceneGraph which has its own dependencies. In nutshell, depending on your distribution, you would need following packages to be installed.

• Development package of libopenscenegraph

• libQGLViewer-2.3.15-py. Install instructions here

• PyQGLViewer0.10 (first install libQGLViewer-2.3.15-py) and untar contents.

  $ cd / PyQGLViewer0.10 $ python setup.py build # to compile $ python setup.py install # to install on your system $ python setup.py bdist # to create a binary distribution

On Ubuntu, following packages should suffice:

$ sudo apt-get install python-qt4-dev python-qt4-gl libopenscenegraph-dev python-sip-dev
libqt4-dev 

Travis

We use Travis-CI to build MOOSE after every commit. You can see .travis.yml file in our repository. It has all instructions to build MOOSE on Ubuntu-12.04 64bit server.