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IMAGIC error

Added by Jason de la Cruz over 13 years ago

Hello,

Appion version '2.1.3'.

I am getting the following error at command line when running the script for IMAGIC Angular Reconstitution (bootstrappedAngularReconstitution.py --description="imagic"...):

...
Traceback (most recent call last):
File "/usr/local/bin/bootstrappedAngularReconstitution.py", line 1360, in ?
AAR = automatedAngularReconstitution()
File "/usr/lib/python2.4/site-packages/appionlib/appionScript.py", line 81, in init
self.checkConflicts()
File "/usr/local/bin/bootstrappedAngularReconstitution.py", line 127, in checkConflicts
apDisplay.printError("$IMAGIC_ROOT directory is not specified, please specify this in your .cshrc / .bashrc")
File "/usr/lib/python2.4/site-packages/appionlib/apDisplay.py", line 56, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
$IMAGIC_ROOT directory is not specified, please specify this in your .cshrc / .bashrc
...

I was about to enter the following command in my .bashrc, then I realized that I don't know the root directory of IMAGIC:

export IMAGIC_ROOT=/?

I appreciate your help.

Thanks,
--Jason


Replies (4)

RE: IMAGIC error - Added by Maarten P almost 7 years ago

Hi,

I'm having the same issue.

I tried installing ImageMagick myself via ftp.imagemagick.org//pub/ImageMagick/ImageMagick.tar.gz.
Looking at the source, appion seems to need .e files in a "stand" folder. I'm unable to find anything which provides these files.

I did a automatic appion installation.

Do I need an older version of ImageMagick?

Thanks,
Maarten

RE: IMAGIC error - Added by Sargis Dallakyan almost 7 years ago

Hi Maarten,

This is a different IMAGIC https://www.imagescience.de/imagic.html. It's not Googleable unless you search for imagic cryo em.

It's a commercial package.

RE: IMAGIC error - Added by Maarten P almost 7 years ago

Hi Sargis,

I found imagic before, but it did not solve my problem. I couldn't find any package with "stand/testim.e" inside for example. Few questions;

1) Why isn't imagic installed by the centosAutoInstallation.py, while "appionlib/apIMAGIC.py" needs the .e files (I try to run "topologyAlignment.py .. --jobtype=partalign ..")?
2) Do I need to install imagic to let appion work? Or do I miss something else?

Thanks!

RE: IMAGIC error - Added by Sargis Dallakyan almost 7 years ago

Hi Maarten,

You don't need to install imagic to let appion work. There is a HIDE_IMAGIC variable that you can set to true in myamiweb/config.php

The centosAutoInstallation.py can't install imagic because imagic is a commercial package. Part of the IMAGIC32/license.txt reads:

2. Software licence

2.1 Object
After the Customer has paid the licence fee, ImSc grants the Customer a
personal, non-transferable and non-exclusive right ("licence") to use and store
the software and program modules described in the Licence Agreement on a single
designated computer or workstation at a single location. The licence will
terminate at the duration time specified in the Licence Agreement and/or if the
Customer destroys all versions and copies of the licensed software. The licence
will also terminate, without the necessity of a written notice from ImSc, if the
Customer does not comply with any term or condition of this Agreement.

    (1-4/4)