How to Update from v16 (Linux)¶

The changes from v1.6 requires update of all in-house components of Leginon, dbemtools and database
but not the mrctools.
Don't forget that you need to also update the packages on the microscope-controlling computer
since the pyScope update need to be synchronized.

See Installation Troubleshooting and Leginon Bulletin Board searching
for "install" if you run into problems.

Packages required from NRAMM¶

All Leginon (and Appion) packages distributed from NRAMM are not under one svn control called myami.

A few updates are needed for preparation of python 3.0 compatibility where the method for importing module is changed. They will still run under python 2.4 and up.
Here are the packages you need to install with python installer

SVN subPackage Name	Reason for update:
numextension	package import method change
libcv	package import method change
leginon	new features
pyami	new features
sinedon	required for updating database
pyscope	new method for creating pythoncom modules
imageviewer	debug

Download myami (contains Appion and Leginon) using one of the following options:

Option 1: 3.4 version (Current release)¶

• We have switched to git for version control.
  

  git clone -b myami-3.4 https://emg.nysbc.org/git/myami myami
  

  
  Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Option 2: beta-release version (Used and updated at NRAMM daily with newest features that may not yet documented)¶

• We have switched to git for version control.
  

  git clone -b myami-beta https://emg.nysbc.org/git/myami myami
  

  
  Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Option 3: Development version (For true developer to play with)¶

• We have switched to git for version control recently. trunk and future release branches will be available with git clone
• unstable with latest features

 
This contains features that may still be under development. It is not supported and may not be stable. Use at your own risk.

git clone -b trunk https://your_redmine_username@emg.nysbc.org/git/myami myami

• your_redmine_username is required if you intend and have permission to push changes to our repository. Please ask the development team if you would like to contribute.*

Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Perform system check if you can't remember where you have installed your Leginon before.¶

cd /your_download_area/myami/leginon
python syscheck.py

You should have all the supporting packages installed for v1.6. If you see any lines like "*** Failed...", then you have something missing. Otherwise, everything should result in "OK".

Install Appion Packages¶

Install the appion python package¶

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 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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< Download Appion/Leginon Files | Perform system check >

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Move your existing processing python packages to a backup directory:¶

At the beginning of the syscheck.py output, the location of the exisiting Leginon folder is shown. Although new installation overwrite the old in most cases, problem has been observed in the past. Therefore, it is best to remove the old files from the path before new installation. Better yet, copy into a backup folder because we need some configuration files from them.

For example, your Leginon folder is at /usr/lib/python/site-packages/Leginon

cd /usr/lib/python/site-packages
mkdir Leginon1_6_backup
mv Leginon Leginon1_6_backup

Be aware that in some cases the installed package name is different (capitalized) from your svn package name and that numextension amd libCV are not in its own subdirectory in the python library but just the compiled .so files

Install Appion Packages¶

Install the appion python package¶

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 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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< Download Appion/Leginon Files | Perform system check >

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Copy your Leginon1.6 sinedon.cfg to the new installation¶

• Find your sinedon.cfg. Depending on your previous setting, look in the directories listed here in order:
  *your home directory as described in syscheck.py
  *The sinedon directory where it is called from. If unsure, start python command line and type these to find out:
  

  python> import sinedon
  python> sinedon

• If sinedon.cfg reside in the installed sinedon subpackage, you should copy it from your Leginon1,6 backup to the new installation.
  

  cd /your_default_python_installation_path
  cp Leginon_1_6_backup/sinedon/sinedon.cfg sinedon
  

Back up all your databases¶

We will be doing a database update that is not backward compatible, Make sure you back up all your current databases before performing the update

• mysqldump -u usr_object your_leginon_database > leginondb_1_6_backup_today's_date
• mysqldump -u usr_object your_project_database > projectdb_1_2_backup_today's_date
• .... do the same to any of your processing databases if you have installed and used Appion 1.0

Install updated Web viewers and tools¶

See Install the Web Interface section in Complete Installation Chapter to put the new web tools (Now under subpackage myamiweb) to document root for the web server. The Setup Wizard will take you through the steps to create config.php and to create and initialize values for the new tables.

Run database update scripts¶

cd /your_download_area/myami/dbschema
python schema-r12857.py
python schema-r13713.py
python schema-r14077.py

The first one update UserData and GroupData so that new data viewing and processing privileges can be enforced
The second is a wide-scale change on database schema many on appion processing databases, and some on projectdata and leginondata.

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How to Update from v1.6 (Microscope Windows Computer) >

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