Metadata-Version: 2.1
Name: relion-yolo-it
Version: 0.2.3
Summary: Updated relion_it with cryolo wrappers
Home-page: UNKNOWN
Author: Donovan Webb
Author-email: donovan.webb@diamond.ac.uk
License: GPLv2
Description: #####################################################################################################
        ##                                                                                                  #
        ##                               relion_it with crYOLO support                                      #
        ##                                                                                                  #
        #####################################################################################################
        
        relion_it is now running with python 3.6.8!  In options you can choose to pick via the crYOLO
        general model or with the relion auto picker.  CrYOLO runs as an external job after ctfFind. Relion
        then takes the particle coordinates found by crYOLO and then further processes them.  Particles
        appear as a manual pick job in the relion gui and can be viewed there.
        
        
        Normal usage for Diamond:
        
        1. module load EM/cryolo/yolo_it       # Prepares python environment for relion_it and crYOLO
        
        2. dls_yolo_relion_it                  # This opens a gui with options
        
        
        Requirements for external use:
        
        1. CrYOLO and Relion 3.0 installed.
        
        2. Conda Environment for crYOLO and Relion
        
        3. Edit paths in options.py for your MotionCor2 and Cryolo general model
        
        4. Run by: cryolo_relion_it.py --gui
        
        
        Scripts being use:
        
         - cryolo_relion_it.py: The main script that dls_yolo_relion calls. This houses the main pipeline
                and calls to all the other scripts.
        
         - CryoloPipeline.py: The crYOLO pipeline. This runs as a subprocess and exectutes many repeated
                times to Import, MotionCorr, CtfFind, crYOLO pick, Extract... as new movies are
                collected. As Relion 3.0 does not support external job types the YOLO pipeline is in fact 3
                seperate pipelines chained together.
        
         - CryoloExternalJob.py: Reads Relion star files and makes a directory that crYOLO can execute
                particle picking from.
        
         - CorrectPath.py: After crYOLO has picked particles, the coordinate star files must be placed in a
                directory tree that Relion is expecting. This does that!
        
         - CryoloFineTuneJob.py: After 2D classification, good classes can be selected to fine tune the
                cryolo general model. After the finetuning, crYOLO uses this new model to pick future
                particles in the current run.
        
         - options.py: Basic options for relion_it to run with.
        
         - qsub.sh: Cluster submit script for crYOLO.
        
         - qtemplate.sh: Cluster template for crYOLO. If using cluster must have template create a
                         '.cry_done' file so that the pipeline knows that cryolo has finished.
        
        
        Note: Fine-tuning requires good 2D classes to be picked by hand after first 2D iteration
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Natural Language :: English
Requires-Python: ==3.6.8
Description-Content-Type: text/plain
