How to Update from v35 (Linux)¶

Upgrade processing server¶

Install PyMySQL that replaces the usage of mysql-python¶

PyMySQL:

pip install PyMySQL==0.10.1

Download myami-3.6 source code¶

git clone -b myami-3.6 http://emg.nysbc.org/git/myami myami-3.6

Install Appion/Leginon Packages¶

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

cd /your_download_area
cd myami-3.6
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". If necessary, you can enter a specific package directory and run the python setup command manually. For example, if sinedon failed to install, you can try again like this:

cd sinedon
sudo python setup.py install

Move leginon.cfg/instruments.cfg/sinedon.cfg/dmsem.cfg if it was saved with the old installation. In general, the installation would have put it in /etc/myami. Therefore, you do not have to do anything.¶

Run this script to find out where it was:

 
cd /your_download_area/myami/leginon/
./configcheck.py

If the script can not find leginon.cfg, and you found a copy of leginon.cfg in $PYTHONSITEPKG/leginon/config from the last installation, move that leginon.cfg to $PYTHONSITEPKG/leginon.

Run Database Update Script¶

Running the following script will indicate if you need to run any database update scripts.

cd /your_download_area/myami/dbschema
python schema_update.py

This will print out a list of commands to paste into a shell which will run database update scripts.
You can re-run schema_update.py at any time to update the list of which scripts still need to be run.

• Changes should be minimal.

Upgrade web server¶

Rename your current myamiweb at the document root of the web server to something else as a backup.

(optional) install the 3.6 version of pyami as it is done on processing server and restart redux server (The changes in pyami do not affect web server)¶

Install updated Web viewers and tools¶

See Install the Web Interface section in Complete Installation Chapter to put the new myamiweb tools to document root for the web server. There is no need to run WebToolSetupWizard, however. See below.

Copy config.php from your older myamiweb backup to the new myamiweb.¶

Import new versions of Leginon Applications¶

Old version of MSI Leginon applications will still run but without new feature. Use the Web administrator tool to import new version as shown in Steps_involved_in_the_installation Step for "Import Applications".

If you want to use Tiltwrangler through web interface, please follow the instruction in¶

Tilt-wrangler launcher in appion

How to Update from v3.5 (Instrument Computer) >