Install EMAN2/SPARX¶

It is best to install EMAN2/SPARX from source, so that do not have conflicts with having two different versions of python on your system. Binaries of EMAN2/SPARX all come with their own python pre-installed.

This documentation assumes you are using CentOS 6 (written as of CentOS 6.2)

Install require pre-packages for EMAN2 compiling¶

yum based packages¶

• Make sure EPEL is install, if not go here: Download additional Software (CentOS Specific)
• Use yum to install devel libraries:
  

  sudo yum install fftw-devel gsl-devel boost-python numpy \
   PyQt4-devel cmake ipython hdf5-devel libtiff-devel libpng-devel \
   PyOpenGL ftgl-devel db4-devel python-argparse openmpi-devel
  

bsddb3¶

Additionally you need to install the python-bsddb3 library (not available via YUM). I just use the pypi easy_installer, yum will never know.

sudo easy_install bsddb3

pyMPI¶

I think this is a dead module (latest version from 2008), but it is required for some EMAN2/SPARX functions, including sxisac.py

• Download pyMPI from here:
  http://sourceforge.net/projects/pympi/files/pyMPI/2.5%20beta/
• Extract the contents:
  

  tar zxvf pyMPI-2.5b0.tar.gz

• Compile:
  

  cd pyMPI-2.5b0
  ./configure --with-includes=`python-config --cflags` --with-libs=`python-config --ldflags`
  make
  
  h2. Download the source
  
  # To download the source code go to the link:
  #* http://blake.bcm.edu/emanwiki/EMAN2
  # Click on *"Current stable version - direct link"*
  # Go under the heading "Source" at bottom of page
  # Click to download the *eman-source-2.xx.tar.gz* file (as of August 2012, 2.xx is 2.06)
  
  h2. Work with the source
  
  # go to the directory with the source code
  # extract the archive:
  <pre>
  tar zxvf eman-source-2.06.tar.gz
  </pre>
  # go into directory
  <pre>cd EMAN2/src/build</pre>
  # start configure script:
  <pre>cmake ../eman2/</pre>
  #* Note: alternatively you can run @ccmake ../eman2/@ and configure all the parameters
  # start compiling:
  <pre>make</pre>
  # install to directory:
  <pre>sudo make install</pre>
  
  h2. Set environmental variables
  
  h3. bash
  
  <pre>sudo nano /etc/profile.d/eman2.sh</pre>
  
  <pre>
  export EMAN2DIR=/usr/local/EMAN2
  export PATH=${EMAN2DIR}/bin:${PATH}
  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
  export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin
  </pre>
  
  h2. Test to see if code works
  
  see http://blake.bcm.edu/emanwiki/EMAN2/FAQ/EMAN2_unittest
  
  <pre>
  cd EMAN2/test/rt
  ./rt.py
  </pre>
  
  h2. Documentation
  
  * http://blake.bcm.edu/emanwiki/EMAN2/Install
  * http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ
  
  ______
  
  [[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]]
  
  ______