Skip to content

Processing Server External Packages Installation

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

  1. Configure .appion.cfg
  2. Install External Packages
  3. MotionCor2
  4. Install Gctf
  5. Install CtfFind. See Install Grigorieff lab software
  1. Compile FindEM

Required for 2D classification and other functions

  1. Install EMAN (Only works for CentOS 6)
  2. Install EMAN2
  3. Install SPIDER
  4. Install Xmipp (Xmipp2 Only works for CentOS 6)
  5. Install UCSF Chimera
  6. Install Ace2
  7. Install Imod
  8. Install Protomo2
  9. Install EM Hole Finder

Older packages, install only if you still want to use them

  1. MotionCorr (optional)
  2. Install SIMPLE

Testing

  1. Test Appion