Leginon

Since Appion wraps software packages like protomo and need to create input to them using pre-existing knowledge from information obtained at the last step that are saved in the appion database, it is different from a simple interface into the software you are used to run. When Appion does not have the input data type to start a process, the menu will not show the function. For example, if there is no particle picked and committed to the database with Appion, you won't see the menu for making a stack.

In the case of Appion tomography pipeline, it works only on data collected with Leginon tomography and have a query into Leginon database to check existence of any tilt series in the session and also uses the tracking results during data collection to initialize protomo alignment. If you have not collected any data that way, you won't get the menu for starting tomography alignment, even if you have the software available. I have been considering allowing uploaded tilt series to be used, but haven't got around to make it true since the images alone is not enough in this case.

As far as troubleshoot the missing link, if you expect an Appion sub-menu to be available at your currently available data type, let us know. You can also check the logic in myamiweb/processing/inc/menuprocessing.php Search for the wording of the expected menu and then follow its link to the actual MySQL query. It is not straight forward at that level, unfortunately.

I have yet to find a "submit" link, only "just show command." I cannot readily find anything related in myamiweb/processing/inc/menuprocessing.php

Hi, Cheri,

At the revision you have (r15323), Submit button is shown only if you log in to the webserver, assuming that it would be the same as the login to the processing host, on the top right corner of the window. The part that controls this behavior is in inc/processing.inc. To assume webserver login to be the same as the processing host one is not ideal and it was fixed in r15575, a few revision after the one you have now. If Harry does not like you to login to webserver like most sys admin we encounter, he can update the myamiweb to r15644. r15644 is being used by another group, and should be reasonably stable.

Just show command is a handy way to get going for finding out if the appion processing program will actually do a good job on your data without the gui complication. Copy and paste the command into a text terminal that is already logged into the processing host should start Appion script running. If that works, "submit" will work if it successfully ssh into the processing host.

Anchi

We still cannot ssh to webserver. Please see Harry's post.