== Installing a Python Virtual Environment for Chimera ==

Get a [http://www.cgl.ucsf.edu/chimera/download.html#daily daily build of Chimera].  In the examples below, it was a linux 64-bit build from 2010-08-05.  To run the installation (accept all the defaults in the prompts):

{{{
$ cd ~/Downloads/
$ chmod +x chimera-alpha-linux_x86_64.exe
$ sudo chimera-alpha-linux_x86_64.exe
}}}

This installation used sudo privileges to install into the default path, {{{/opt/UCSF/Chimera64-2010-08-05}}}.  If you don't have sudo priviledges, install to an alternative path where you have write permissions.  I like to have it install symlinks into
{{{
$ ls -al /usr/local/bin/chimera*
lrwxrwxrwx 2 root root 42 2010-08-24 14:45 /usr/local/bin/chimera -> /opt/UCSF/Chimera64-2010-08-05/bin/chimera
lrwxrwxrwx 1 root root 42 2010-08-05 14:53 /usr/local/bin/chimera-2010-08-05 -> /opt/UCSF/Chimera64-2010-08-05/bin/chimera
}}}

In the following notes, a few environment variables are set to simplify executing the new installation programs.  If your installation path is different, you will need to set the CHIMERA environment variable to your path.
{{{
$ export CHIMERA=/opt/UCSF/Chimera64-2010-08-05
$ export PATH=$PATH:$CHIMERA/bin/ 
$ export LD_LIBRARY_PATH=$CHIMERA/lib
}}}

Now get the setuptools package installed into the python system that was specifically built and installed for Chimera.  Note the following has some version specific details that need attention for any current installation.  At the time of writing, this installation used a specific daily-build of Chimera (2010-08-05) and a specific version of setuptools for the version of python that was built for Chimera (python2.7).

{{{
$ sudo -i
# export CHIMERA=/opt/UCSF/Chimera64-2010-08-05
# export PATH=$PATH:$CHIMERA/bin/ 
# export LD_LIBRARY_PATH=$CHIMERA/lib
# wget http://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg
# sh setuptools-0.6c11-py2.7.egg --prefix=$CHIMERA
}}}

If you prefer to use distribute instead of setuptools, try the following:
{{{
$ sudo -i
# export CHIMERA=/opt/UCSF/Chimera64-2010-08-05
# export PATH=$PATH:$CHIMERA/bin/ 
# export LD_LIBRARY_PATH=$CHIMERA/lib
# curl -O http://python-distribute.org/distribute_setup.py
# $CHIMERA/bin/python2.7 distribute_setup.py
...
Processing distribute-0.6.14-py2.7.egg
creating /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg
Extracting distribute-0.6.14-py2.7.egg to /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages
Adding distribute 0.6.14 to easy-install.pth file
Installing easy_install script to /opt/UCSF/Chimera64-2010-08-05/bin
Installing easy_install-2.7 script to /opt/UCSF/Chimera64-2010-08-05/bin

Installed /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg
Processing dependencies for distribute==0.6.14
Finished processing dependencies for distribute==0.6.14
After install bootstrap.
Creating /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info
Creating /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/setuptools.pth
}}}


Now use these tools to install any python package into the Chimera specific python distribution.  For example, install the virtualenv package, like so:

{{{
$ sudo -i
# export CHIMERA=/opt/UCSF/Chimera64-2010-08-05
# export PATH=$PATH:$CHIMERA/bin/ 
# export LD_LIBRARY_PATH=$CHIMERA/lib
# $CHIMERA/bin/easy_install-2.7 virtualenv
Searching for virtualenv
Reading http://pypi.python.org/simple/virtualenv/
Reading http://virtualenv.openplans.org
Best match: virtualenv 1.4.9
Downloading http://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.4.9.tar.gz#md5=c49067cab242b5ff8c7b681a5a99533a
Processing virtualenv-1.4.9.tar.gz
Running virtualenv-1.4.9/setup.py -q bdist_egg --dist-dir /tmp/easy_install-eNIuwN/virtualenv-1.4.9/egg-dist-tmp-blYuR8
warning: no previously-included files matching '*.*' found under directory 'docs/_templates'
Adding virtualenv 1.4.9 to easy-install.pth file
Installing virtualenv script to /opt/UCSF/Chimera64-2010-08-05/bin

Installed /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/virtualenv-1.4.9-py2.7.egg
Processing dependencies for virtualenv
Finished processing dependencies for virtualenv
}}}


Now that virtualenv is installed in the Chimera python distribution, we can setup any additional custom virtual environments to add python packages into the development environment.  As a regular user, the following will create a Chimera-specific development environment in ~/src/chimera-virtualenv:

{{{
$ export CHIMERA=/opt/UCSF/Chimera64-2010-08-05
$ export PATH=$PATH:$CHIMERA/bin/ 
$ export LD_LIBRARY_PATH=$CHIMERA/lib
$ mkdir -p ~/src
$ cd ~/src
$ $CHIMERA/bin/virtualenv chimera-virtualenv
New python executable in chimera-virtualenv/bin/python2.7
Also creating executable in chimera-virtualenv/bin/python
Installing setuptools.................done.
$ ls -al chimera-virtualenv/
total 20
drwxr-xr-x  5 dweber dweber 4096 2010-08-24 14:05 ./
drwxr-xr-x 45 dweber dweber 4096 2010-08-24 14:05 ../
drwxr-xr-x  2 dweber dweber 4096 2010-08-24 14:05 bin/
drwxr-xr-x  2 dweber dweber 4096 2010-08-24 14:05 include/
drwxr-xr-x  3 dweber dweber 4096 2010-08-24 14:05 lib/
}}}

Once this virtual environment is created, it can be activated and deactivated with the following commands (note how the system prompt changes to indicate that we have entered and left the virtual environment).

{{{
$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ deactivate
$ 
}}}

Now start the Chimera build of python and import the chimera module, like this:

{{{
$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ python
Python 2.7 (r27:82500, Aug  5 2010, 14:15:36) 
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> import os
>>> os.getenv('CHIMERA')
'/opt/UCSF/Chimera64-2010-08-05'
>>> sys.path.append(os.path.join(os.getenv('CHIMERA'), 'share'))
>>> sys.path.append(os.path.join(os.getenv('CHIMERA'), 'lib'))
>>> import chimera
>>> chimera.version.version
'alpha version 1.5 (build 31152) 2010-08-05 19:55:24 GMT'
>>> for s in sys.path: print s
... 

/home/dweber/src/chimera-virtualenv/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg
/home/dweber/src/chimera-virtualenv/lib/python2.7/site-packages/pip-0.7.2-py2.7.egg
/home/dweber/src/chimera-virtualenv/lib/python27.zip
/home/dweber/src/chimera-virtualenv/lib/python2.7
/home/dweber/src/chimera-virtualenv/lib/python2.7/plat-linux2
/home/dweber/src/chimera-virtualenv/lib/python2.7/lib-tk
/home/dweber/src/chimera-virtualenv/lib/python2.7/lib-old
/home/dweber/src/chimera-virtualenv/lib/python2.7/lib-dynload
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/plat-linux2
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-tk
/home/dweber/src/chimera-virtualenv/lib/python2.7/site-packages
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/distribute-0.6.14-py2.7.egg
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/virtualenv-1.4.9-py2.7.egg
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/PIL
/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info
/opt/UCSF/Chimera64-2010-08-05/share
/opt/UCSF/Chimera64-2010-08-05/lib
>>>
}}}


To add additional packages into the virtual environment, try using pip.

{{{
$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ pip help
Usage: pip COMMAND [OPTIONS]

Options:
  --version             show program's version number and exit
  -h, --help            Show help
  -E DIR, --environment=DIR
                        virtualenv environment to run pip in (either give the
                        interpreter or the environment base directory)
  -s, --enable-site-packages
                        Include site-packages in virtualenv if one is to be
                        created. Ignored if --environment is not used or the
                        virtualenv already exists.
  -v, --verbose         Give more output
  -q, --quiet           Give less output
  --log=FILENAME        Log file where a complete (maximum verbosity) record
                        will be kept
  --proxy=PROXY         Specify a proxy in the form
                        user:passwd@proxy.server:port. Note that the
                        user:password@ is optional and required only if you
                        are behind an authenticated proxy.  If you provide
                        user@proxy.server:port then you will be prompted for a
                        password.
  --timeout=SECONDS, --default-timeout=SECONDS
                        Set the socket timeout (default 15 seconds)

Commands available:
  bundle: Create pybundles (archives containing multiple packages)
  freeze: Output all currently installed packages (exact versions) to stdout
  help: Show available commands
  install: Install packages
  search: Search PyPI
  uninstall: Uninstall packages
  unzip: Unzip individual packages
  zip: Zip individual packages
}}}


Now for something adventurous, installing the [http://packages.python.org/spyder/ spyder] python-IDE.  (In the example below, sip and PyQt are installed with sudo privileges only because Chimera was installed with those privileges.  If you install Chimera without sudo privileges, try to run {{{make install}}} commands instead of {{{sudo make install}}}.)

{{{
$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ cd ~/Downloads
(chimera-virtualenv)$ wget http://www.riverbankcomputing.co.uk/static/Downloads/sip4/sip-4.10.5.tar.gz
(chimera-virtualenv)$ tar zxvf sip-4.10.5.tar.gz
(chimera-virtualenv)$ cd sip-4.10.5
(chimera-virtualenv)$ python configure.py
(chimera-virtualenv)$ make
(chimera-virtualenv)$ sudo make install
(chimera-virtualenv)$ cd ..
(chimera-virtualenv)$ wget http://www.riverbankcomputing.co.uk/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.4.tar.gz
(chimera-virtualenv)$ tar zxvf PyQt-x11-gpl-4.7.4.tar.gz
(chimera-virtualenv)$ cd PyQt-x11-gpl-4.7.4
(chimera-virtualenv)$ python configure.py --no-designer-plugin --qmake=/usr/bin/qmake-qt4
(chimera-virtualenv)$ make
(chimera-virtualenv)$ sudo make install
}}}

That should satisfy the dependencies for [http://packages.python.org/spyder/ spyder].  So, try to install spyder, like so:
{{{
$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ pip install spyder
}}}

OK, if that works, then try to setup the environment and run spyder.

{{{
$ source ~/src/chimera-virtualenv/bin/activate
(chimera-virtualenv)$ export TCL_LIBRARY="$CHIMERA/lib/tcl8.6"
(chimera-virtualenv)$ export TCLLIBPATH="{$CHIMERA/lib}"
(chimera-virtualenv)$ unset TK_LIBRARY
(chimera-virtualenv)$ unset TIX_LIBRARY
(chimera-virtualenv)$ export LD_PRELOAD=libotf.so
(chimera-virtualenv)$ export PATH=$PATH:$CHIMERA/bin
(chimera-virtualenv)$ unset PYTHONHOME
(chimera-virtualenv)$ unset PYTHONPATH 
(chimera-virtualenv)$ spyder
}}}