Launching on-the-fly processing

Pre-prescribed on-the-fly processing pipelines are offered through the relipy.run_pipeline command line utility. For RELION 3 this is a version of the relion_it.py script packaged with RELION 3.1 modified to allow the use of crYOLO for particle picking and the running of various IceBreaker jobs for the estimation of ice thickness within micrographs. For RELION 4 the logic of this pipeline has been rewritten using the CCP-EM pipeliner. Below are breif instructions for the condiguration and running of these pipelines.

RELION 3

An options file is required to run the pipeline. A default options file called relion_it_options.py can be generated with the command

relipy.print_options

The parameters in this file should be edited to suit both the data collection parameters and system setup. This file should be provided to the relipy.run_pipeline command to start processing:

relipy.run_pipeline -f <path to relion_it_options.py> -m <path to data directory> -d <path to project directory>

The data directory is the top level directory containing the movies or micrographs to be imported. The project directory is the RELION project directory. A symlink will be created from a Movies directory in the project directory to the specified data directory.

Processing can be stopped by removing the *_RUNNING files written to the project directory.

RELION 4

The general setup is the same for the RELION 4 pipeline. The flag --version 4 should be added to the run command. By default 2D classification is done using the EM algorithm but can be switched to VDAM by specifying do_class2d_vdam to be True in the relion_it_options.py file.

The Relion 4.0 pipeline will stop automatically after all movies have been processed and no new movies have appeared within a timeout period (this is set to two days be default and can be changed by specifying the timeout in seconds with the --timeout flag for relipy.run_pipeline). Otherwise the pipeline can be stopped by creating a file called stop.stop int he project directory.

To restart a stopped processing pipeline (only available for RELION 4):

relipy.run_pipeline --version 4 -f <path to relion_it_options.py> -m <path to data directory> -d <path to project directory> --continue

It is difficult to guarantee that this will always work as intended.