/open-ephys-install-instructions

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Installation of the Open Ephys GUI on a 32-bit Debian machine

These steps are correct as of Nov 6, 2015

They were pieced together from https://open-ephys.atlassian.net/wiki/display/OEW/Linux and other sources of information.

You will need to build the program from source, as compiled binaries currently only exist for 64-bit Linux. The steps are:

  1. Obtain the source code
  2. Install the ZeroMQ library
  3. Install the latest HDF5 library version
  4. Install the Open Ephys GUI

Obtain the Open Ephys source

Clone the repository (forked at the margoliashlab github account under ‘GUI’) into the appropriate folder (your choice):

wget https://github.com/open-ephys/GUI/archive/v0.3.6.tar.gz

Install the ZeroMQ library.

First, add the PPA to the package manager’s sources list:

sudo add-apt-repository ppa:chris-lea/zeromq

Because PPAs are a Ubuntu-specific feature, you need to modify the appropriate source list file to make it look like you’re updating from a machine running Ubuntu. The file (assuming you’re running Debian 7.0 ‘wheezy’) is

/etc/apt/sources.list.d/chris-lea-zeromq-wheezy.list

This file will contain the following two lines:

deb http://ppa.launchpad.net/chris-lea/zeromq/ubuntu wheezy main
deb-src http://ppa-launchpad.net/chris-lea/zeromq/ubuntu wheezy main

You need to change both instances of ‘wheezy’ to the name of a valid Ubuntu version. I used ‘trusty’. No other changes are needed. (The name of the .list file itself, funnily enough, doesn’t need to be changed.)

Now update the package list information

sudo apt-get update

Now you can install the libraries themselves. For the version of the Open Ephys GUI current at the time of this writing, you need version 3 of the ZeroMQ API. This is specified in the command below:

sudo apt-get install libzmq3-dbg libzmq3-dev libzmq3

Install the HDF5 library

The version of the Open Ephys GUI current as of this writing requires a version of the HDF5 library higher than 1.8.11. Currently, updating the HDF5 library using apt-get on Debian only updates to 1.8.8.9, so you’ll need to build this library from source.

Download link for source: http://www.hdfgroup.org/HDF5/release/obtainsrc.html

If you want to be able to keep running jill software, it is a good idea to only install this later version of the HDF5 library locally instead of globally. This will prevent this later version from interfering with the library bindings jill modules use to create .arf files. (This may not be an issue, but I wasn’t about to risk it the first time.)

Place the source tarball in a folder (not /usr/bin! /usr/local might be ok. I installed it in a folder called ‘hdf5-current’ in my home folder) of your choice and extract it (if tar complains that it’s zipped, add ‘z’ to the ‘-xf’):

tar -xf [tarball filename]

cd to the new extracted directory and run the configure script. For the ‘--prefix’ argument, provide the directory containing the tarball and extracted source code directory. Make sure to include the ‘--enable-cxx’ flag, or make will only install the C bindings:

./configure --prefix=[wherever you installed it] --enable-cxx

Now there are four make invocations, each one of which may take some time (tens of minutes in total, in my case):

make
make check
sudo make install
sudo make check-install

The last thing to do is to make sure the current session’s environment variables contain the appropriate paths to this new HDF5 library. You need to set three environment variables:

export CPLUS_INCLUDE_PATH=[path to hdf5 directory]/include
export LIBRARY_PATH=[path to hdf5 directory]/lib
export LD_LIBRARY_PATH=[path to hdf5 directory]/lib

Build the Open Ephys GUI itself

First, run the dependency installation script in the GUI/Resources/Scripts folder:

sudo ./install_linux_dependencies.sh

Then copy the device interface rules file (in the same directory as above) to the system’s udev (not dev) folder and refresh the udev service:

sudo cp 40-open-ephys.rules /etc/udev/rules.d
sudo service udev restart

cd to GUI/Builds/Linux and run make

make

The installation should go smoothly if you’ve followed the above instructions. The binary to run the GUI is called ‘open-ephys’ and resides in GUI/Builds/Linux/build.

Running the Open Ephys GUI

The last wrinkle involves those environment variables you set above. If you close your current session and restart it, they won’t be set any more. Setting them to be updated at login isn’t a great idea, because they could interfere with jill modules’ access to the older HDF5 library. To get around this, the easiest thing to do is write a short shell script that sets them and then starts the Open Ephys GUI in the same fork. You would then use this script to start the GUI, much like how we use Kyler’s intan-interface.sh script.

You can copy the script I wrote from my directory on modeln, or you can copy it in its entirety here (with appropriate modification of paths for your installation):

#! /bin/bash

export CPLUS_INCLUDE_PATH=[path to hdf5 directory]/include
export LIBRARY_PATH=[path to hdf5 directory]/lib
export LD_LIBRARY_PATH=[path to hdf5 directory]/lib

[path to open-ephys folder]/GUI/Builds/Linux/build/open-ephys

Don’t forget to chmod it to allow execution:

chmod a+x open-ephys.sh

NOW you’re done.

Appendix A: Some Reading for the Curious or Desperate

The build instructions from the Open Ephys devs are linked at the top of this document. Further information I found helpful in creating this guide can be found at the following links. These may prove helpful if you run into trouble and can’t solve it immediately.