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Carl Negro, 09/10/2015 02:21 PM
Install Appion Packages¶
Install the appion python 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 /path/to/myami-VERSION/appion sudo python setup.py install --install-scripts=/usr/local/bin/appion
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'
Check permissions:¶
Verify that the all users have executable permission for rctacquisition.py. It may be necessary to run:
chmod 755 ./leginon/rctacquisition.py
Set additional appion environment variables¶
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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Updated by Carl Negro about 9 years ago · 38 revisions