How to Update from v22-redux (Linux)¶

2.2-redux version is installed on CentOS6 and uses redux. Its upgrade to Leginon/Appion 3.0 release does not require os upgrade.

Upgrade processing server¶

Download myami 3.0 source code¶

svn co http://emg.nysbc.org/svn/myami/branches/myami-3.0/

Install Appion/Leginon Packages¶

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

cd /your_download_area
cd 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". 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 if it was saved with the old installation.¶

Run this script to find out where it was:

 
cd /your_download_area/myami/leginion/
./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.

Upgrade web server¶

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

install the 3.0 version of redux and pyami.¶

Follow Install_Redux_image_server instruction but note the following¶

• The old version in python's site-packages directory will be overwritten.
• The old redux.cfg, if in the installation, is still applicable.
• Make sure you run fftwsetup.py if you have odd-dimension camera such as Gatan K2.

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¶

All MSI Leginon applications need to be upgraded or it will not run. Use the Web administrator tool to do this as shown in Steps_involved_in_the_installation Step for "Import Applications".

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How to Update from v2.2-redux (Instrument Computer) >