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Instructions for Installing Pre-requisites for Brainhacking 101

The following sections contain instructions for downloading the software needed to participate in the Brainhack courses. If you have any difficulties installing any packages, help will be available at the Brainhack Installfests. If the following packages are unavailable for your platform or you do not wish to install the software, you can follow the tutorials by downloading only the X2Go client (instructions in the AWS section) and logging into an Amazon cloud instance.

GitHub

Software to install

  • git

Debian/Ubuntu Linux

Type the following command in a terminal:

sudo apt-get install -y git

CentOS/RHEL

Type the following command in a terminal:

sudo yum install -y git

Mac OS X

Download the Xcode Command Line Tools here (you will need to obtain an Apple ID if you do not have one already). Git is included as one of the tools. (If you have trouble making a secure connection to Apple, check for any anti-virus software that might be blocking web connections, such as Sophos.)

Windows

Download Git for Windows here.

Python

Software to install

  • Anaconda (Python 2.7)
  • Pip
  • IPython
  • Jupyter
  • Numpy
  • Scipy

You should download a scientific Python distribution such as Anaconda, which has binaries for Linux, Mac OS X, and Windows that can be found here. Make sure that you download a binary with Python 2.7 (not Python 3.4). Anaconda comes with a useful command for managing packages (conda) that complements the conventional Python package manager (pip) well. Installing some packages on Mac OS X is particularly difficult without using a Python distribution such as Anaconda. The following installation commands assume the use of Anaconda, although you may also want to try out Enthought Canopy.

After you have installed Anaconda, install the Python package manager, IPython, Jupyter, and NumPy/SciPy by typing the following command in a terminal:

conda install pip ipython jupyter numpy scipy

The proceeding Nibabel, Nilearn, AWS classes assume that you have installed Python.

Nibabel

Download Python if you have not already using the instructions above. Then type the following in a terminal:

pip install nibabel

Nilearn and Plotting

Download Python and nibabel if you have not already using the instructions above. Then type the following in a terminal:

pip install scikit-learn matplotlib
pip install -U --user nilearn

Neurodebian

Software to install (for VM)

  • Virtualbox

Instructions for adding the Neurodebian repositories to Debian-based Linux distributions are here.

Downloads for Virtualbox (needed to import the Neurodebian Virtual Machine) can be found here.

Instructions for installing the Neurodebian Virtual Machine are here.

AWS

Software to install

  • AWS Command Line Interface
  • Boto
  • Starcluster
  • X2Go Client
  • Cyberduck (or CloudExplorer for Linux users)

Download Python if you have not already using the instructions above. Then type the following in a terminal to install the AWS Command Line Interface, boto and Starcluster:

pip install awscli boto starcluster

You will also need to configure the AWS CLI by following the instructions here.

X2Go will allow you to pull up a desktop session on a running instance of an Amazon Machine Image. To install the the X2Go client for Linux, Mac OS X, or Windows, follow the instructions here.

Note for OS X: We have encountered difficulties with X2Go and keyboard mappings when using older versions of Apple X11. If you come across such issues (i.e., control keys not working), try updating to the latest version of XQuartz using this link.

Cyberduck will allow you to browse Amazon S3 buckets (storage areas for files). You can download Cyberduck for Mac OS X and Windows here.

Linux users can use CloudExplorer. To install Cloud Explorer, first install its dependencies:

Debian/Ubuntu Linux

sudo apt-get install openjdk-8-jre openjdk-8-jdk ant

CentOS/RHEL

sudo yum -y install git java-1.8-openjdk java-1.8.0-openjdk-devel ant
sudo update-alternatives --config java
sudo update-alternatives --config javac

Then type the following commands in a terminal:

git clone https://github.com/rusher81572/cloudExplorer.git
cd cloudExplorer
ant

To start CloudExplorer, make sure that you are within the cloudExplorer directory and then type:

java -jar dist/CloudExplorer.jar