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.

Testing

After installing on any of the systems below, you should test to make sure it's working. While we have unit testing, it is mainly for those compiling from source. Instead, we suggest just running the following 3 basic tests:

• e2speedtest.py (will also give you the relative speed to expect from your machine)
• e2workflow.py (if the GUI pops up, it's working)
• e2proc2d.py anyimagefile bdb:test (anyimagefile is any 2d image or stack supported by eman2, this will make sure the database works)

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, I suppose the EMAN2 will be install into home directory. So I use my home directory "/home/gtang" as an example. EMAN2 provide four nightly builds for Linux: eman2.nightly.linux.tar.bz2 and eman2.daily.linux.tar.bz2 are for 32 bit Linux (i386). eman2.daily.linux64.tar.bz2 and eman2.daily.linux64.gcc4.tar.bz2 are for 64 bit Linux (x86_64). The gcc4 version requires glibc version at least 2.5. We recommand you install gcc4 version of EMAN2 unless you are running a linux release several years ago. If you are not sure, you can check you glibc version by '/sbin/ldconfig -V'. If you are not sure your linux is 32 bit or 64 bit. You can check with command 'uname -r'. If you see x86_64 that means your linux is 64 bit. Otherwise it's 32 bit linux. To install this binary release, for example, on 64 bit Linux: download eman2.daily.linux64.gcc4.tar.bz2 to your home directory.

$tar xvjf eman2.daily.linux64.gcc4.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 in eman2.bashrc 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.

NOTE: The binary EMAN2 use the Python interpreter ship with EMAN2. The eman2-installer will automatically change python interpreter in python files in EMAN2 to (for my installation):

#!/home/gtang/EMAN2/python/Python-2.6.5-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.

Note: Ubuntu user

In the workflow.py main window, if you choose "Single Particle Reconstruction"->"CTF"->"Interactive Tuning - e2ctf", if you cannot see the CTF curve show up(CTF curve window is blank), please install a package called "freeglut" in your synaptic package manager. While this is true for other Linux, ubuntu does not install this package by default.

Windows

• If you have installed previous version of EMAN2. Please uninstall it and remove a directory called c:\tmp\eman2db-***.
• 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 Python2.7, 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 conflict.

• 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++ 2008 Redistributable downloaded from Microsoft or from here Download Visual C++ 2008 redistributable runtime library here..

  • 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 uses PyQt4 as GUI toolkit. It has conflict with Matlab R2007b, you need uninstall Matlab or install it in a different account, i.e. not system wide install.

• Windows user please ignore this warning message, "WARNING: Using the out of date 'bsddb' module instead of bsddb3. Consider installing newer berkeleydb and bsddb3."

• 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, in case the EMAN2 installer does not set them up for you successfully.

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.

• 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

• 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

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

right click "my computer"->properties->Advanced->Environment Variables, in "system variables"edit the "path" entry,
-> then add following value into it: C:\EMAN2\bin;C:\EMAN2\lib;C:\EMAN2\python\Python27;C:\EMAN2\python\Python27\Lib\site-packages\PyQt4\bin.
Create a new system variable PYTHONPATH, add following value into it: C:\EMAN2\lib;C:\EMAN2\bin. (note: In the example I suppose you install
EMAN2 into C:\ directory, change it accordingly if you install EMAN2 in other directory.)