Before I again start taking the mongodb apart, I wonder if there is a documentation of the command line interface that is mentioned in the general reference for cryoSPARCv2. I am also fine with a very rough list of options or just the source code of the parser…
cryosparcm cli <command> - runs the command using the cryosparc cli cryosparcm icli - drops the current shell into an interactive cryosparc shell that connects to the master processes and allows you to interactively run cli commands
If so, we are planning a public roll-out of API-style documentation for additional functions, but there is currently no timeline for when this will be released. We will make sure you find out as soon as it does!
I know how to run an already set up job (set up in the webapp) and how to clear it, but I don’t know how to create a new job from command line. I’ve seen from the discussions (with Scipion) that it is possible (cryosparcm cli make_job), but I’d like to know exactly how it works. Do you have a documentation for the different type of jobs? I’m mainly interested in particle set import, 2D classification, ab-initio reconstruction and 3D refinement.
Thank you in advance for your help!
Due to the non-existing documentation of the cmd interface, I have started reverse engineering it from the cryosparc source code. Additionally, I looked into cryosparcs MongoDB to figure out how to read/insert some custom information. The result is a simple Python library to interface with cryosparc2 which enables me to do exactly the things you want to via python scripts. However, this libary is still quite crude (too crude for GitHub ). If you are interested, send me a message and I can send you the library.