Ensure Cuda 8.0 is installed properly on the host machine.
Copy this repository with the command git clone http://github.com/nysbc/motioncor2-docker
Install Docker: https://docs.docker.com/install/
Install Nvidia-Docker: https://github.com/NVIDIA/nvidia-docker
Download and install MotionCor2: http://msg.ucsf.edu/em/software/motioncor2.html
Copy and unzip the MotionCor2 zip file into the motioncor2-docker directory.
Change directories to motioncor2-docker.
Run the build script: ./build.sh
The build script should take 1-2 minutes if Docker and Nvidia-Docker are installed properly.
Run MotionCor2 with the command ./motioncor2. You should see the output from MotionCor2:
Usage: MotionCor2 Tags
-InMrc
1. Input MRC file that stores dose fractionated stacks.
2. It can be a MRC file containing a single stack collected
in Leginon or multiple stacks collected in UcsfTomo.
3. It can also be the path of a folder containing multiple
MRC files when -Serial option is turned on.
-InTiff
1. Input TIFF file that stores a dose fractionated stack.
-OutMrc
1. Output MRC file that stores the frame sum.
2. It can be either a MRC file name or the prefix of a series
MRC files when -Serial option is turned on.
-ArcDir
1. Path of the archive folder that holds the archived raw
stacks with each pixel packed into 4 bits.
2. The archived stacks are saved in MRC file with the gain
reference saved in the extended header.
3. The rotated and/or flipped gain reference will be saved
if -RotGain and or -FlipGain are enabled.
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