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Install EMAN2 » History » Revision 32

Revision 31 (Neil Voss, 08/13/2012 09:32 PM) → Revision 32/87 (Neil Voss, 08/13/2012 09:33 PM)

h1. 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) 

 h2. Install require pre-packages for EMAN2 compiling 

 h3. yum based packages 

 * Make sure EPEL is install, if not go here: [[Download additional Software (CentOS Specific)]] 
 * Use yum to install devel libraries: 
 <pre> 
 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 
 </pre> 

 h3. 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. 
 <pre> 
 sudo easy_install bsddb3 
 </pre> 

 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. Install MyMPI for SPARX MPI functions 

 see http://sparx-em.org/sparxwiki/MPI-installation 
 or https://www.nbcr.net/pub/wiki/index.php?title=MyMPI_Setup 

 h2. Documentation 

 * http://blake.bcm.edu/emanwiki/EMAN2/Install 
 * http://blake.bcm.edu/emanwiki/EMAN2/FAQ/eman2BuildFAQ 

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 [[Install EMAN|< Install EMAN 1]] | [[Install SPIDER|Install SPIDER >]] 

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