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Binary Installation on Ubuntu 10.04 (lucid), 10.10 (Maverick) and 11.04 (Natty), 11.10 (Oneiric), 12.04 (precise), 12.10 and 14.04 (trusty)

Warning: The 14.04 is now working.

We have set up a ppa to distribute deb files for ubuntu. Add the ppa to your system in a terminal by enter:

sudo add-apt-repository ppa:christophe-pradal/openalea
sudo add-apt-repository ppa:christophe-pradal/vplants
sudo add-apt-repository ppa:christophe-pradal/alinea
sudo apt-get update

Note: if you get a `add-apt-repository: command not found` install first:

sudo apt-get install software-properties-common python-software-properties

Then install all openalea and vplants components and their dependencies:

sudo apt-get install python-openalea python-vplants python-alinea
sudo apt-get install python-vplants.tissue # On Ubuntu 12.10 not 14.04

Finally, type a command to update your environment variables( do not execute this command as root):

alea_config

That's it. You can run visualea or lpy as well as aml.

Compilation from sources

If you want to install from the source, follow the instructions below.

If you do not have access to the SVN repository, see also installation_from_targz

Ubuntu 12.10

 Ubuntu 12.10

If starting from FRESH installation, install SVN ipython and vim

  sudo apt-get install libzmq-dev ipython ipython-qtconsole ipython-notebook vim subversion python-all python-dev

OpenAlea, VPlants and Alinea depends on several packages. Install them

Dependencies

  # requested by openalea/vplants
  sudo apt-get install python-setuptools python-qt4 python-qt4-gl python-matplotlib python-scipy python-pandas python-rpy2  libreadline-dev freeglut3 bison flex g++ scons libqt4-dev libqt4-opengl-dev libqhull-dev libreadline-dev pkg-config freeglut3-dev libann-dev liblapack-dev libmpfr-dev libblas-dev freeglut3-dev libboost-all-dev python-sip-dev pyqt4-dev-tools python-qt4-dev python-soappy python-skimage python-sklearn python-sphinx libeigen2-dev

compilation

Create a local environment to install all the Python packages locally ($HOME/.local)

cd ~/.local
mkdir lib bin include  
cd lib
mkdir python2.7 python2.7/site-packages

Edit the file ~/.pydistutils.cfg

[install]
prefix = /home/<user>/.local

Then edit your ~/.bashrc file:

source ~/.openalea.sh
 
export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATH
export PATH=$HOME/.local/bin:$PATH

Checkout the sources (change username and possibly the path to the SVN sources; here we check out the trunk)

  svn co --username <username> https://scm.gforge.inria.fr/svn/openalea/trunk openalea

Compile and install openalea

  cd openalea
  make install
  cd ..
  alea_config --install-dyn-lib=/home/<user>/.local/lib

Compile and install vplants (if you have read access to the repository)

  svn co --username <username> https://scm.gforge.inria.fr/svn/vplants/vplants/trunk vplants
  cd vplants
  python multisetup.py install

Compile and install alinea (if you have read access to the repository)

  svn co --username <username> https://scm.gforge.inria.fr/svn/openaleapkg openaleapkg
  cd openaleapkg
  python multisetup.py install  # multisetup is an openalea script

Ubuntu 9.10

 Ubuntu 9.10

Note however that the python version is 2.6.4 and that you must therefore use BoostPython 1.41
See Ubuntu 12.10 instructions.

Name of dependencies change a little bit. So to install dependencies please follow this steps:

Dependencies

  # requested by openalea/vplants
  sudo apt-get install python-qt4 python-qt4-gl # graphical environement of visualea
  sudo apt-get install python-matplotlib python-scipy # some scientific packages
  sudo apt-get install python-rpy2 # install many dev librairies
  sudo apt-get install dvipng  texlive-latex-extra # install latex dependencies
  sudo apt-get install libreadline5 libglut  # PlantGL dependencies
  

Because we want to compile from the sources, we also need development libraries:

  # dependencies for vplants compilation
  sudo apt-get install bison flex g++ scons          # PlantGL compilation
  sudo apt-get install libqt4-dev                    # PlantGL compilation
  sudo apt-get install libqhull-dev libncurses5-dev  # PlantGL compilation
  sudo apt-get install libreadline5-dev libglut-dev  # PlantGL compilation
  sudo apt-get install sip4 python-sip4 python-sip4-dev # PyQGLViewer
  sudo apt-get install pyqt4-dev-tools # to compile PyQGLViewer
  sudo apt-get install python-qt4-dev # to compile PyQGLViewer
 
  sudo apt-get install python-soappy # for developers who want to upload eggs 
  

Compilation

See Ubuntu 12.10 instructions.

To build vplants, you need libboost-python 1.41. This version is not available on Ubuntu 9.10. So we provide an egg:

  alea_install boostpython

Ubuntu 8.10

See Ubuntu 8.04 instructions

Ubuntu 8.04

 Ubuntu 8.04

If starting from FRESH installation, install SVN and virtualenv

  sudo apt-get install python-setuptools # to install virtualenv
  sudo easy_install virtualenv
  sudo apt-get install ipython vim subversion

OpenAlea, VPlants and Alinea depends on several packages. Install them

  # requested by openalea/vplants
  sudo apt-get install python-qt4 python-qt4-gl # graphical environement of visualea
  sudo apt-get install python-matplotlib python-scipy # some scientific packages
  sudo apt-get install python-rpy # install many dev librairies
  sudo apt-get install dvipng  texlive-latex-extra # install latex dependencies
  
  

Because we want to compile from the sources, we also need development libraries:

  # dependencies for vplants compilation
  sudo apt-get install bison flex g++                # PlantGL compilation
  sudo apt-get install libqt4-dev                    # PlantGL compilation
  sudo apt-get install libcgal-dev                   # to compile PlantGL with CGAL
  sudo apt-get install libqhull-dev libncurses5-dev  # PlantGL compilation
  sudo apt-get install libreadline5-dev libglut-dev  # PlantGL compilation
  sudo apt-get install libboost-python1.34.1 libboost-python-dev   # PlantGL, stat_tool compilation
  sudo apt-get install sip4 python-sip4 python-sip4-dev # PyQGLViewer
  sudo apt-get install pyqt4-dev-tools # to compile PyQGLViewer
  sudo apt-get install python-qt4-dev # to compile PyQGLViewer
 
  sudo apt-get install python-soappy # for developers who want to upload eggs 

Compile and install vplants. You may need the following link to lib mysqlclient_r.

  #posssibly you want to add missing links 
  ln -s /usr/lib/libmysqlclient_r.so.15.0.0 /usr/lib/libmysqlclient_r.so
  ln -s /usr/lib/libsqlite3.so.0 /usr/lib/libsqlite3.so

Then, follow the instructions from the Ubuntu 9.04 section

Pre-compiled version

FIXME This is relevant for 0.6.X release only

On Fedora 10, Ubuntu 8.10 and Mandriva, the eggs (precompiled version) that are available on the gforge and accessible from the openalea gui installer should be compatible with the third-party librairies provided by the Linux version.

On older systems such as Ubuntu8.04, the third libraries may not be compatible: Vplants packages won't work. You will need to recompile by yourself from the sources using the tar.gz files available on the GForge.

In the Ubuntu8.04 case, we provide a pre-compiled version for the release 0.6.2, which can be installed as follows assuming that you have installed openalea packages as usual:

Get the file VPlants.Source-0.6.2.r6021.ubuntu8.04-eggs.tar.gz either from GForge or directly and copy this file into a directory. Go to that directory and type:

wget --no-check-certificate https://gforge.inria.fr/frs/download.php/18128/VPlants.Source-0.6.2.r6021.ubuntu8.04-eggs.tar.gz
tar xvfz VPlants.Source-0.6.2.r6021.ubuntu8.04-eggs.tar.gz;
easy_install *egg

Then, you need to be sure that your LD_LIBRARY_PATH is correct and contains the path to the library just installed in /usr/lib/python2.5/site-packages/VPlants*/lib. for instance if you installed the packages as root:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/python2.5/site-packages/VPlants.AmlObj-0.6.2-py2.5-linux-i686.egg/lib:/usr/lib/python2.5/site-packages/VPlants.Mtg-0.6.2-py2.5-linux-i686.egg/lib:/usr/lib/python2.5/site-packages/VPlants.PlantGL-0.6.2-py2.5-linux-i686.egg/lib:/usr/lib/python2.5/site-packages/VPlants.Aml-0.6.2-py2.5-linux-i686.egg/lib:/usr/lib/python2.5/site-packages/VPlants.PlantGL-0.6.2-py2.5-linux-i686.egg/lib:/usr/lib/python2.5/site-packages/VPlants.Sequence_analysis-0.6.2-py2.5-linux-i686.egg/lib:/usr/lib/python2.5/site-packages/VPlants.Stat_Tool-0.6.2-py2.5-linux-i686.egg/lib/:/usr/lib/python2.5/site-packages/VPlants.Tool-0.6.2-py2.5-linux-i686.egg/lib/:/usr//lib/python2.5/site-packages/VPlants.PlantGL-2.8.3-py2.5-linux-i686.egg/lib/:/usr//lib/python2.5/site-packages/VPlants.Tree_matching-0.6.2-py2.5-linux-i686.egg/lib/
 
documentation/user/ubuntu.txt · Last modified: 2014/12/11 16:41 by user   Back to top
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