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.