How to Update from v21 (Linux)¶

Download myami 2.2.x source code¶

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.

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 if it was saved with the 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.

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

Install updated Web viewers and tools¶

You will not need to upgrade php mrc tools.

See Install the Web Interface section in Complete Installation Chapter to put the new myamiweb tools to document root for the web server.

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

Step through setup wizard in the myamiweb on your server¶

The Setup Wizard will take you through the steps to update config.php If the wizard does not have the privilege to modify the file at the last step, copy the displayed result to an text editor and save as config.php to replace the olde one.

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.

Assigning Cs value for each TEM used by Leginon¶

schema-r15653.py that shows up in the list of required update when schema-update.py is run is used to assign individual spherical aberration constant (Cs) values to different microscope. Please find out what these values are in advance before running the script to save time.

Running the python script will prompt you at each TEM you have used so far so that you can enter the value in unit of millimeter

The Cs value also need to match what is set in pyscope/instrument.cfg before you will be able to acquire more images. See How to Update from v2.1 (Microscope Windows Computer)

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How to Update from v2.1 (Microscope Windows Computer) >

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