No Applications in the Database when Leginon starts on Ubuntu

To whom it may concern,

Now I have succeeded installing leginon on the TEM computer. However, when I tried to test Leginon with simulator as it describes on the website, I faced a very strange problem.

When I start the Leginon program on Ubuntu via running "start-leginon.py", the Leginon wizard runs okay. However, when I tried to click Application -> Run, it says "Error: No application in the database“. I just checked the config file of leginon and it did not mention anything about the applications in the database. Could you help me solve this problem?

Thanks a lot in advance!

Replies (5)

RE: No Applications in the Database when Leginon starts on Ubuntu - Added by Anchi Cheng about 12 years ago

The Ubuntu installation wiki does not go through all installation steps. Only ones involving OS differences. There are a few things handled by myami autoinstaller for CentOS 5 in Leginon/Appion 2.2 that you may miss easily following the manual installation. I am sure that you will find a few more of these after this one. I can't predict what they will be. Therefore, let's start at what will solve your current problem.

Applications in question are Leginon Applications. See Terminology. Go to Steps involved in the installation using administration tools on your web server and go to the section for "Import Applications" and import Leginon applications you would like to use that came with your Leginon download.

RE: No Applications in the Database when Leginon starts on Ubuntu - Added by Long Gui about 12 years ago

Hi Anchi,

Thanks a lot for your help. This problem was solved via copying Application files into Leginon fold. Currently the file sharing system works nicely but we have a new problem in redux showing the final results.

While I tried to view our captured images, the frame shows

"Failed
redux failed to return anything."

Then I applied server trouble shooting tools "http://localhost/myamiweb/test/checkwebserver.php"

The trouble shooting result says that we are probably missing MRC PHP extension since the "Display Images" are not visible.

So we planned to install MRC PHP extension. We have installed php-GD and FFTW3-devel. But during installation, after I typed into "./configure

The screen shows "configure: error: gd.h not found."

I think one possible explanation might be we installed php5-gd instead of php-gd on Ubentu 12.04. Would you please help me with this problem? Thanks a lot!

Thanks,
Long

RE: No Applications in the Database when Leginon starts on Ubuntu - Added by Long Gui about 12 years ago

Hi Anchi,

I am sorry that I did not noticed the change of the myami fold change on the Ubuntu installation site.

The version I have downloaded on Sep 21st was "myami-trunk" but the current version is "myami-2.2-redux" Is the current version much better than the previous one?

Thanks.
Long

RE: No Applications in the Database when Leginon starts on Ubuntu - Added by Anchi Cheng about 12 years ago

Hi, Long,

Don't install MRC PHP extension. php 5.3 that comes with Ubuntu can not compile php-mrc, which is why we told you to install the redux version. I will have Jim give you more testing on redux.
You can start with direct command on running redux as described in Redux.

Anchi

RE: No Applications in the Database when Leginon starts on Ubuntu - Added by Anchi Cheng about 12 years ago

For Leginon purpose only, myami-trunk you downloaded is likely fine since there was not heavy development around the time you downloaded. However, if you are to do any processing with Appion, myami-trunk in Septemper 2012 is not stable because a lot of development was going on there.

For users like you who are not involved in development, we recommend the branches. Current branch that will be easiest to install on Ubuntu 12.x and CentOS 6.x is myami-2.2-redux. For CentOS 5.x, use myami-2.2.

Anchi

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