Make sure you have the
conda-forge channel active, because some of our
dependencies are not available in the default channels.
brainiak channel to install:
conda install -c brainiak -c defaults -c conda-forge brainiak
We support Linux and MacOS with Python version 3.5 or higher. Most of the dependencies will be installed automatically. However, a few need to be installed manually.
Install the following packages (Ubuntu 16.04 is used in these instructions):
apt install build-essential libgomp1 libmpich-dev mpich python3-dev \ python3-pip python3-venv
Install updated version of the following Python packages:
python3 -m pip install --user -U pip
--user flag, which instructs Pip to not overwrite system
files. You must add
$HOME/.local/bin to your
$PATH to be able to run
the updated Pip, e.g., by adding the following line to
and launching a new login shell (e.g., logout or execute
Install the Xcode Command Line Tools:
brew from https://brew.sh. If you already have
the output of the following command to make sure it is working:
Then install the following:
brew install llvm cmake mpich python3
Note that if your MacOS does not have
gcc (a prerequisite of
it will take a long time (perhaps over an hour) to install
gcc from source for you.
You must instruct programs to use this
clang version at
One way to do this, which
works for most programs, is setting the
CC environment variable. You can
add the following lines to
you have one). For them to take effect, you must logout or launch a new login
export CC=/usr/local/opt/llvm/bin/clang export CXX=/usr/local/opt/llvm/bin/clang++
In addition, you also need to specify the directories that the newly installed
will seek for compiling and linking:
export LDFLAGS="-L/usr/local/opt/llvm/lib "\ "-Wl,-rpath,/usr/local/opt/llvm/lib $LDFLAGS" export CPPFLAGS="-I/usr/local/opt/llvm/include $CPPFLAGS"
Install updated versions of the following Python packages:
python3 -m pip install -U pip
Installing and upgrading¶
The Brain Imaging Analysis Kit is available on PyPI. You can install it (or upgrade to the latest version) using the following command:
python3 -m pip install -U brainiak
python setup.py install might fail. It is recommended to install using pip.
Note that you may see a
Failed building wheel for brainiak message (issue
#61). Installation will proceed despite this failure. You can safely ignore it
as long as you see
Successfully installed at the end.
Until we reach version 1.0, we will only support the latest released version. Therefore, if you have a problem with an older version, please upgrade to the latest version before creating an issue on GitHub.