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Anchi Cheng, 09/10/2013 10:26 AM
Testing auto-installation¶
- Click on [test dataset]
- You should see two images in an image viewer. If they are not visible, run the troubleshooter by clicking on [Troubleshoot].
- Click on [Home] to return to the start page.
- Click on Project DB and you should find a GroEL Demo project that has been created for you.
- Return to the [Home] page.
- Click on [Image Viewer] and you should find the sample images that have been added to a Sample Session in the Demo Project.
- Click on [Processing] to begin running image processing jobs on the sample GroEL images.
- Following the directions in Process Images is a good test of the installation.
- You will want to continue by installing the third party processing packages which are required for many of the features supported by Appion:
Appion scripts interact with external packages in one of the two ways: Executing a shell command, or through python call. The name of the file in the call may not be the same as the standard installation as described by the package distributor.
If it is accessed from shell, you should either create soft link (preferred) or rename the file you downloaded (not best practice since you may get confused later. Test its accessibility from the environment you would run appion script.
For example, ctffin4 of whatever version would typically installed in /usr/local/bin. The executable file in there is called ctffind4.exe. You should do
cd /usr/local/bin ln -s ctffind64.exe ctffind4
Next time, when you start a shell, try:
which ctffind4
It should be able to find the link and the actual executable file.ctffind64.exe
For files called through python, the file need to be in the environment variable PYTHONPATH You can test it in the appion environment with an import test.
python python> import deProcessFrames
Program/module call alias name in Appion (myami-3.3, myami-beta branches, and trunk)¶
Package alias table¶
Those not mentioned here uses the original names in the call.
program package name | version | appion executable alias | Accessible |
MotionCor2 | 1.0.2 | motioncor2 | shell |
motioncorr v2.0 from Purdue | 2.0 | dosefgpu_driftcorr | shell |
DE_process_frames.py | 2.7.1 | deProcessFrames.py | pythonpath |
ctffind4 | 4.1.5 | ctffind4 | shell |
Gctf | 1.06 | gctfCurrent | shell |
ctftilt | 1.5 | ctftilt.exe | shell |
FindEM | 20/10/01 | findem64.exe | shell |
Gautomatch | 0.53 | gautomatch | shell |
Spider | 18.10 | spider | shell |
frealign | 9.11 | frealign_v9.exe and frealign_v9_mp.exe | shell |
xmipp2 cl2d* | 2.4 | xmipp_mpi_class_averages | shell |
xmipp3 cl2d* | 3.1 | xmipp_classify_CL2D | shell |
EMAN1 proc2d | 1.9 | proc2d | shell |
- default environment is xmipp2. All other xmipp functions wraps around xmipp2.
- xmipp3 conflict with xmipp2 is resolved in appion/bin/runXmipp3CL2D.py with a line of code
csh -c 'modulecmd python load xmipp/3.1'
Change it if desired.
Installation¶
External Package requirement of Appion scripts
Required for preprocessing pipeline up to stack making for Relion/CryoSparc¶
- Configure .appion.cfg
- Install External Packages
- MotionCor2
- Install Gctf
- Install CtfFind. See Install Grigorieff lab software
Recommended for preprocessing pipelin particle picking¶
Required for 2D classification and other functions¶
- Install EMAN (Only works for CentOS 6)
- Install EMAN2
- Install SPIDER
- Install Xmipp (Xmipp2 Only works for CentOS 6)
- Install UCSF Chimera
- Install Ace2
- Install Imod
- Install Protomo2
- Install EM Hole Finder
Older packages, install only if you still want to use them¶
- MotionCorr (optional)
- Install SIMPLE
Testing¶
Updated by Anchi Cheng about 11 years ago · 1 revisions