Install Appion Packages¶

Install the appion python package¶

The pysetup.py script above did not install the appion package. Since the appion package includes many executable scripts, it is important that you know where they are being installed. To prevent cluttering up the /usr/bin directory, you can specify an alternative path, typically /usr/local/bin, or a directory of your choice that you will later add to your PATH environment variable. Install appion like this:

cd appion
sudo python setup.py install --install-scripts=/usr/local/bin

Install all the myami python packages except appion using the following script:¶

cd /path/to/myami-VERSION/myami
sudo ./pysetup.sh install

That will install each package, and report any failures. To determine the cause of failure, see the generated log file "pysetup.log".

Packages installed by pysetup.sh¶

Package Path:
pyami
myami_test
sinedon
leginon
pyscope
imageviewer
modules/numextension
modules/radermacher
modules/libcv

alternatively, install a specific package in turn¶

If necessary, you can enter a specific package directory and run the python setup command manually. For example, if pyami failed to install, you can try again like this:

cd pyami
sudo python setup.py install

python-site-package-path: where the installed python packages went:¶

Python installer put the packages you installed into its site-packages directory. This enables all users on the same computer to access them. The easiest way to discover where your installed package is loaded from by python is to load a module from the package using interactive python command lines like this:

Start the python command line from shell:

python

Import a module from the package. Let's try pyami here. All packages installed through the above setup.py script should go to the same place.
At the python prompt (python>) type:

import pyami

If the module is loaded successfully, call the module attribute path (two underscrolls before "path" and two underscrolls after) will return the location of the module it is loaded from

pyami.__path__
['/usr/lib/python2.6/site-packages/pyami']

In this case, /usr/lib/python2.6/site-packages/ is your python-site-package-path. If you go to that directory, you will find all the packages you just installed.

Save this value as an environment variable for use later, for bash:

export PYTHONSITEPKG='/usr/lib/python2.6/site-packages'

or C shell

setenv PYTHONSITEPKG '/usr/lib/python2.6/site-packages'

Finally, you will need to set the the MATLABPATH environment variable in order to get the Appion utilities that use Matlab to work.
For bash:

export MATLABPATH=$MATLABPATH:<your_appion_directory>/ace

or C shell

setenv MATLABPATH $MATLABPATH:<your_appion_directory>/ace

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< Perform system check | Configure leginon.cfg >

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