Installation

Requirements

• Python 2.7
• numpy >= 1.3.0
• quantities >= 0.9.0
• neo >= 0.2.1
• sqlalchemy >= 0.7.8
• sqlalchemy-migrate >=0.7.2
• scipy >=0.10
• matplotlib>=1.1.0
• pyqtgraph >=223
• guidata >=1.4.1
• PyQT4 >= 4.9
• joblib >=0.6.4
• tables >=2.3.1
• pywavelets (pywt)
• python-sklearn >=0.11

Optional but important:

• psycopg2 (for postgreesql)
• mysqldb (for mysql)
• blosc (for fast compression)
• python-snappy (for really fast compression)
• lz4 (for really really fast compression)

You can also instal:

• a mysql server
• a postrgesql server

but OpenElectrophy also work in file mode or with SQLite db.

Linux

For debian/ubuntu users, open a terminal:

Step 1, dependencies:

sudo apt-get install python python-scipy python-numpy python-matplotlib python-qt4 python-mysqldb python-pip python-psycopg2 python-dev gfortran python-pywt python-sqlalchemy python-migrate python-tables python-joblib  python-guidata python-sklearn
pip install quantities neo

Step 2, OpenElectrophy:

You have two choices:

1. From pypi (this is the latest stable release):

   sudo pip OpenElectrophy

2. From source (this includes up-to-date features and bugfixes as they are added):

   sudo apt-get install git
   git clone git@github.com:OpenElectrophy/OpenElectrophy.git
   cd OpenElectrophy
   sudo python setup.py install

Client under Windows with winpython

Steps:

1. Download winpython http://code.google.com/p/winpython/

2. Choose win3? or amd64 if you have win64

3. Choose for the path. Example: C:\winpython-2.7.3.amd64

4. in this path lanch control panel. This tool help you to install package. (See http://code.google.com/p/winpython/wiki/WPPM)

5. Download manually all that depencies and install them withh winpython wontrol panel (choose the good platform win32 or amd64):

   • quantities (http://pypi.python.org/pypi/quantities)
   • neo (http://pypi.python.org/pypi/neo)
   • sqlalchemy-migrate (http://pypi.python.org/pypi/sqlalchemy-migrate)
   • joblib (http://pypi.python.org/pypi/joblib)
   • blosc (http://pypi.python.org/pypi/blosc/1.0.3)
   • MySQL-python (http://www.lfd.uci.edu/~gohlke/pythonlibs/)
   • pywavelet (http://pypi.python.org/pypi/PyWavelets/)

6. Dowlaod pyqtgraph http://www.pyqtgraph.org/:

   • rename pyqtgraph-dev-r223-32.exe to pyqtgraph-223.0.0.win32-py2.7.exe
   • or rename pyqtgraph-dev-r223-32.exe to pyqtgraph-223.0.0.amd64-py2.7.exe

   Instal it with control panel.

7. Dowload OPenElectrophy (http://pypi.python.org/pypi/OpenElectrophy) and install it.

8. In the controal panel> Advanced>register your python

Warning

python-snappy and lz4 are hard to install under windows because they need a compiler at installation times. So database access can be slower.

Client under OSX

..TODO

Test your installation

If you want to test the UI of OpenElectrophy :

• Linux : open a console (terminal) type:

  startOpenElectrophy
  

• Windows : click (or make a shortcut on your desktop) on:

  C:\\winpython-2.7.3.amd64\\python-2.7.3.amd64\\Lib\\site-packages\\OpenElectrophy.egg\\EGG-INFO\\scripts\\startOpenElectrophy

If you want to test if OpenElectrophy module is installed, open an ipython interactive console

import OpenElectrophy

MySQL server under linux

Just type this

sudo apt-get install mysql-server

During the installation process, choose a password for root (admin).

MySQL server under Windows

Here you can download binaries for mysql server: http://dev.mysql.com/downloads/

Basic server administration

The basic MySQL administration is quite simple: you only need to create users, one database, and to grant each user access to the database.

You just have to type in a mysql console.

User creation

CREATE USER user IDENTIFIED BY PASSWORD 'password'

Database creation

CREATE DATABASE  db_name

Privileges for the user on this database

GRANT ALL ON db_name.* TO user

Troubleshooting

• Problems for importing big file (>1Go) in MySQL

  If you experience problems for importing heavy file in mysql you should change this parameters in mysql.cnf on server side

  max_allowed_packet=32G

  Some users hd reported that this parameters also cause problem in client side.