Appion

Package executable alias used in 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.

1. Configure .appion.cfg
2. Install External Packages
3. MotionCor for DD camera frame movie drift correction
4. Install EMAN
5. Install EMAN2
6. Install SPIDER
7. Install Xmipp
8. Install UCSF Chimera
9. Install Grigorieff lab software
10. Compile FindEM
11. Install Ace2
12. Install Imod
13. Install Protomo
14. Install EM Hole Finder
15. Install SIMPLE
16. Test Appion