Leginon

That page is outdated. We probably need to put a link to http://msg.ucsf.edu/em/software/motioncor2.html and tell users to install MotionCor2 from that site instead.

MotionCor2 is implemented in myami-beta branch, not 3.2

So, question: should I be implementing the beta branch instead of 3.2? Is that what everyone in the know is doing? I'm not a domain expert, but according to the users, the main purpose of the processing machine is to run motioncor2; so this is a must have. Also, I thought motioncor2 was included as part of Appion. Now I'm confused about what Appion does.

I recommend going with the trunk. Beta brunch is what we use at NYSBC. It's more stable but lucks some of the new features from the trunk. Regarding motioncor2, we can't distribute it with Appion because of the motioncor2 license. Appion provides a wrapper for motioncor2. You can lunch motioncor2 with Appion which will loop over your images and display nicely aligned images on a web-browser.

I disagree unfortunately. trunk is for developer. It can break at any time. beta is used every day and get new features after it is tested in the trunk. MotionCor2 functions are in beta for a while now. If you are giving this to be used in production, you will do better with beta.

Motioncor2 runs by itself as with many of the software packages we wrap in Appion. If all you want is that, then you don't need Appion. Appion is more a system that provides different software package to the users in the same form and helps with organization of the results. It becomes powerful when your need is diverse, not when you only have one need.

motioncor2 is the main software they need to run on this system, but they want all the other stuff, too. Let me see if I can get 3.2 working; if not, I'll take a look at beta. Thanks!

Wait, though. Do I have to use beta if I want motioncor2? I'm still not clear on this point.

Yes, you do.

The replacement is fairly simple since you have done all the database and webserver setup and installed supporting packages.

Mainly:

How_to_Update_from_v32_(Linux)

When I try running

# ./pysetup.sh install

I get

root@kraken:/home/cnsit/leginon/myami-beta# ./pysetup.sh install
Log file: /home/cnsit/leginon/myami-beta/pysetup.log
processing imageviewer... ok.
processing leginon... ************FAILED!!! (see log for details)
processing pyami... ok.
processing pyscope... ok.
processing sinedon... ok.
processing redux... ok.
processing modules/radermacher... ok.
processing modules/libcv... ok.
processing modules/numextension... ok.

Looking at the log file:

########################
processing leginon
########################
python setup.py install
Traceback (most recent call last):
  File "setup.py", line 6, in <module>
    import version
  File "/home/cnsit/leginon/myami-beta/leginon/version.py", line 19, in <module>
    from pyami import gitlib
ImportError: cannot import name gitlib

I'm not sure what caused this, as the directories are being processed in the same order as they were in myami-32. However, this solved the problem:

root@kraken:/home/cnsit/leginon/myami-beta# cd pyami/
root@kraken:/home/cnsit/leginon/myami-beta/pyami# python setup.py install
root@kraken:/home/cnsit/leginon/myami-beta# cd ../leginon/
root@kraken:/home/cnsit/leginon/myami-beta/leginon# python setup.py install

(At least I think it did; the leginon stuff appeared to get installed this time with no complaints.)

That is our fault, this new requirement of gitlib means that pyami needs to go first. created Issue #5164, and will push to beta soon.

Yep. For some reason when I looked at it yesterday my brain told me pyami was already being set up before leginon in pysetup.sh (I think I was too focused on comparing the script to what is in 3.2). When I looked at it again this morning it was obvious what the problem is.

BTW, it looks like upgrading just means overwriting existing .py files. Presumably you should also run cleanpy.sh before doing the upgrade -- that should be in the upgrade documentation. One final point: I'm also assuming that there is a 1-1 relationship between files in 3.2 and files in beta. If not, then the old install probably needs to be deleted entirely before the new version is installed.

Point well taken. We used to tell people to first move the existing installed directory.