Differences between revisions 10 and 16 (spanning 6 versions)

Mac OS X

Mac OS X 10.5 and 10.6 are supported for EMAN2 nightly builds. 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.

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.

Environement Variable Setting For EMAN2

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

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, edit the "path" entry,
-> then add the EMAN2's bin and lib directory into it. Add PYTHONPATH to EMAN's lib directory.

-  ⇤ ← Revision 10 as of 2008-09-29 22:08:46 → 
  Size: 2180
  Editor: DavidWoolford
  Comment:
+   ← Revision 16 as of 2009-11-14 03:40:38 → ⇥
  Size: 3162
  Editor: root
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-Currently, only 10.5 is supported for EMAN2 nightly builds. The nightly snapshot for MAC isn't a nightly snapshot, it's a build from several months ago. If you want to use e2boxer on your MAC you will have to install from source as several critical updates have been committed since then.

Visit the EMAN2 nightly page and download the disk image .dmg package. It includes an EMAN2 directory and a set of installation instructions in INSTALL.txt. The instructions contain a few simple steps to get the EMAN2 build up and running on your machine.
+Mac OS X 10.5 and 10.6 are supported for EMAN2 nightly builds. 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.
-Line 7:
+Line 5:
-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.
+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.
-Line 14:
+Line 11:
-Which Python version you want to choose:
1 - Python 2.5 UCS4
2 - Python 2.5 UCS2
3 - Python 2.4 UCS4
4 - Pyhton 2.4 UCS2
5 - Pyhton 2.3 UCS4
6 - Python 2.3 UCS2
[Default is 1 (Pyhton 2.5 UCS4)]
：
(make your choice here, or type enter for default)}}}
+}}}
-Line 29:
+Line 17:
-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. 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):
+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):
-Line 33:
+Line 26:
-So, you need run this python interpreter for EMAN2. Or if you write script for EMAN2, you need add that line to the beginning of your script.
+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.

= Environement Variable Setting For EMAN2 =

We need set up environment variables like PATH, LD_LIBRARY_PATH and PYTHONPATH for EMAN2 to working 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 
}}}    
 
 2. 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   
}}}

 3. 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.
}}}