All platforms

When upgrading to a newer version, BEFORE downloading/untaring the new version, you MUST run

e2bdb.py -c

This will clean up the cache and make sure you don't have any running EMAN2 jobs while you do the upgrade. While unlikely, failing to do this could result in corruption of some files. If you do forget, and don't want to reinstall the old version, you will need to 'rm -rf /tmp/eman2db-*' to remove all old cache files. Normally this will be safe as long as no EMAN2 programs are actively running, and nothing crashed.

Mac OS X

Mac OS X 10.5 and 10.6 are supported for EMAN2 nightly builds. The build is fully 64 bit on 10.6, and this package is recommended and tested more regularly. Download the appropriate dmg from the nightly build page, copy "EMAN2" to your "/Applications" folder. Instructions on loading the environment variable init script are included in the README.txt file.

There is a visual installation guide that explains the process with screenshots.

Linux

Note: In the following installation instruction, "/home/gtang" is my home directory. You should see your home directory name on your computer. EMAN2 provide two nightly builds for Linux: eman2.nightly.linux.tar.bz2 is for 32 bit Linux (i386). eman2.nightly.linux64.tar.bz2 is for 64 bit Linux (x86_64). To install this binary release, for example, on 64 bit Linux: download eman2.nightly.linux64.tar.bz2 to your home directory.

$tar xvjf eman2.nightly.linux64.tar.bz2
$cd EMAN2
$./eman2-installer

Then you will see at the end of the output:

Please add the following line to the end of your /home/gtang/.bashrc
source /home/gtang/EMAN2/eman2.bashrc

This eman2.bashrc just provide some environment variables for EMAN2 and sparx. You can either add the source line to your .bashrc, or copy all the environment variable setting into your.bashrc file:

gedit /home/gtang/.bashrc

Then add the given source line to the file. Note: if you are using some kind of c shell, you will see the eman2.chsrc file. The binary EMAN2 use the Python interpreter comes with EMAN2. The eman2-installer will automatically change python interpreter in python files in EMAN2 to (for my installation):

#!/home/gtang/EMAN2/python/Python-2.5.1-ucs4/bin/python

So, you need run this python interpreter for EMAN2. Or if you write script for EMAN2, you need to add that line to the beginning of your script.

Windows

• If you plan to install both EMAN1 and EMAN2, EMAN1 must be installed FIRST.

• For windows(XP/Vista/7 32/64), EMAN2 comes with it's own Python2.5, with preinstalled site-packages like PyQt4, PyOpenGL etc., So if you have your own Python installed, you may need uninstall it IF there is a confilict.

• If you have a previous eman2 release installed, please uninstall it before you install a new one.
• After installation, you can open a command prompt and type e2.py.
  • If you get error like:

    • ImportError: DLL load failed: The application has failed to start because its side-by-side configuration is incorrect.

      ImportError: DLL load failed: This application has failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem.

      please install Visual C++ 2005 SP1 Redistributable downloaded from http://ncmi.bcm.edu/ncmi/software/counter_222/software_91/index_html.

  • If you get a python prompt successfully, try typing 'display(test_image())'. You should see an s-shaped image appear on the screen. If so, EMAN2 is working.
• If you double click on one of the icons, and the application doesn't open properly, please try running it from the command-line instead. This will give better error information.

• EMAN2 may still have problems on specific windows machines. If you run into any, please report them to sludtke@bcm.edu

Environement Variable Setting For EMAN2

We need set up environment variables like PATH, LD_LIBRARY_PATH and PYTHONPATH for EMAN2 to work correctly.

These environment variables will be automatically set when you run eman-installer script when you install binary EMAN release.

But for people compile from source and other diagnosis purpose, user may want to know how those environment variables should be set.

1. For sh/bash like shells on Linux/UNIX system (suppose you install EMAN2 under your home directory):

export EMAN2DIR=${HOME}/EMAN2
export PATH=${PATH}:${EMAN2DIR}/bin
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
export PYTHONPATH=${PYTHON_PATH}:${EMAN2DIR}/lib

1. For csh/tcsh like shell on Linux/UNIX system (suppose you install EMAN under your home directory):

setenv EMAN2DIR ${HOME}/EMAN2
setenv PATH ${PATH}:${EMAN2DIR}/bin
setenv LD_LIBRARY_PATH ${EMAN2DIR}/lib    #setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib if you have LD_LIBRARY_PATH set
setenv PYTHONPATH ${EMAN2DIR}/lib         #setenv PYTHONPATH ${PYTHONPATH}:${EMAN2DIR}/lib  if you have PYTHONPATH set

1. For windows system (suppose you install EMAN2 under C:\):

right click "my computer"->properties->Advanced->Environment Variables, edit the "path" entry,
-> then add the EMAN2's bin and lib directory into it. Add PYTHONPATH to EMAN's lib directory.