CP2.0 on Linux

From Cellprofiler Developer Wiki

First, it's worth looking at Building CellProfiler2.0.app on a Mac to understand the prerequisites. A similar approach using pip/virtualenv is probably the easiest way to get many of the required python libraries.

There's a discussion in the forum about using CP2.0 for batch processing.

This is one user's log of getting CP running on Ubuntu 9.10 (note that much of step 9 could be handed via pip/virtualenv, instead):

 1 - Install Ubuntu 9.10 Karmic amd64
 2 - Change /etc/apt/sources.list (see bellow) (must use sudo to change)
 3 - Now, update the packages from sources:
      $ sudo aptitude update
 4 - Update the system:
      $ sudo aptitude dist-upgrade
 5 - Install C/C++ and make packages:
      $ sudo aptitude install build-essential
 6 - Install svn client:
      $ sudo aptitude install subversion
 7 - Get CellProfiler:
      $ svn co https://svnrepos.broadinstitute.org/CellProfiler/trunk/CellProfiler/ <CellProfiler path location>/CellProfiler
 8 - Install and configure Java:
      $ sudo aptitude install java-package sun-java6-bin sun-java6-demo sun-java6-fonts sun-java6-jdk sun-java6-jre sun-java6-plugin sun-java6-source
      $ sudo echo "JAVA_HOME="/usr/lib/jvm/java-6-sun"" >> /etc/environment
      $ sudo echo "LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun/jre/lib/amd64/server" >> /etc/bash.bashrc
      $ sudo echo "export LD_LIBRARY_PATH" >> /etc/bash.bashrc
 9 - Install Cython, numpy, scipy, setuptools, numeric, matplotlib, wxgtk, decorator, mysql, nose and development librarys for Python 
      $ sudo aptitude install cython python-numpy python-scipy python-setuptools python-numeric python-matplotlib python-wxgtk2.8 python-decorator python-mysqldb python-nose python-dev
 10 - Restart system
 11 - Running CellProfiler:
       $ cd <CellProfiler path location>/CellProfiler
       $ python CellProfiler.py
 
 ==========================================
 == /etc/apt/sources.list 
 ==========================================
 deb http://archive.ubuntu.com/ubuntu/ karmic main restricted
 deb-src http://archive.ubuntu.com/ubuntu/ karmic restricted main multiverse universe
 deb http://archive.ubuntu.com/ubuntu/ karmic-updates main restricted
 deb-src http://archive.ubuntu.com/ubuntu/ karmic-updates restricted main multiverse universe
 deb http://archive.ubuntu.com/ubuntu/ karmic universe
 deb http://archive.ubuntu.com/ubuntu/ karmic-updates universe
 deb http://archive.ubuntu.com/ubuntu/ karmic multiverse
 deb http://archive.ubuntu.com/ubuntu/ karmic-updates multiverse
 deb http://archive.canonical.com/ubuntu karmic partner
 deb-src http://archive.canonical.com/ubuntu karmic partner
 deb http://archive.ubuntu.com/ubuntu/ karmic-security main restricted
 deb-src http://archive.ubuntu.com/ubuntu/ karmic-security restricted main multiverse universe
 deb http://archive.ubuntu.com/ubuntu/ karmic-security universe
 deb http://archive.ubuntu.com/ubuntu/ karmic-security multiverse