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 MOOSE from source

If you really want to build MOOSE from source, you can either use cmake (recommended) or GNU make based flow.

Download the latest source code of moose from github or sourceforge.

$ git clone -b master https://github.com/BhallaLab/moose-core

Install dependencies

For moose-core:

• gsl-1.16 or higher.
• libhdf5-dev (optional)
• libsbml-dev (5.9.0, optional)
• python-dev
• python-numpy

Note on libsbml Make sure that libsml is installed with zlib and lxml support. Following instructions are known to work.

- 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 
- sudo make install 

On Ubuntu-12.04 or higher, these can be installed with:

sudo apt-get install python-dev python-numpy libhdf5-dev cmake libgsl0-dev g++ 

NOTE : On Ubuntu 12.04, gsl version is 1.15. You should skip libgsl0-dev install gsl-1.16 or higher manually.

Use cmake to build moose:

$ cd /path/to/moose-core 
$ mkdir _build
$ cd _build 
$ cmake ..
$ 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.

Python3

You just need to one command in previous set of instructions to following

cmake -DPYTHON_EXECUTABLE=/opt/bin/python3 ..

Install

$ sudo make install

Using gnu-make

This may or may not work (not maintained by packager)

You may need to inform make of C++ include directories and library directories if your installed packages are at non-standard location. For example, if your have libsbml installed in /opt/libsbml and the header files are located in /opt/libsbml/include and lib files are located in /opt/libsbml/lib, you can set the environment variables CXXFLAGS and LDFLAGS to include these before calling make:

export CXXFLAGS= -I/opt/libsbml/include
export LDFLAGS= -L/opt/libsbml/lib

Release build:

cd moose
make BUILD=release

Debug build:

cd moose
make BUILD=debug

Python 3K

By default, MOOSE is built for Python 2. In case you want to build MOOSE for Python 3K, you need to pass the additional flag:

PYTHON=3

like:

make BUILD=release PYTHON=3

Installation:

For system-wide installation you can run:

sudo make install

Post installation

Now you can import moose in a Python script or interpreter with the statement:

import moose

If you have installed the GUI dependencies below for running the graphical user interface, then you can run the GUI by double-clicking on the desktop icon or via the main-menu. The squid axon tutorial/demo is also accessible via these routes.

Local-installation

If you do not have permission to install it in system directories, you can let it be where it was built or copy the python subdirectory of MOOSE source tree to a location of your choice and add the path to your PYTHONPATH environment variable. Suppose you have a ~/lib directory where you keep all your locally built libraries, do:

cp -r {moose-source-directory}/python ~/lib/

and add this to your .bashrc file (if you use bash shell):

export PYTHONPATH="$HOME/lib/python":"$PYTHONPATH"

For other shells, look up your shell's manual to find out how to set environment variable in it.