More docs for running jobs with cryosparc-tools

Features and Functionality
1

Hi!

I’m interested in using cryosparc-tools to define cryo-EM workflows that can be run reproducibly, without user intervention, and with external tools. While the documentation for creating and running external jobs is very good, I haven’t found comprehensive documentation for the job_type names and allowed parameters of standard/internal cryoSPARC jobs.

In this old thread about the cryoSPARC cli, there was a reference to /path/to/cryosparc_master/cryosparc_compute/jobs/workflows/buildrun_bench.py. Presumably the logic in this script is still informative for chaining jobs together in cryosparc-tools. However, it doesn’t completely document how each job type can be called and parameterized.

Currently, I am tediously assembling this information from the JSON output in the Metadata tab for each particular job in the web interface, but I’m not positive I’m interpreting things correctly. Is it possible to get documentation that maps job_types and params to jobs/options in the web interface?

best,
Eugene

2

Hi Eugene,

I was facing similar issues a few weeks ago. I found that the build.py file for each job type in /path/to/cryosparc_master/cryosparc_compute/jobs gives all of the parameters that can be used as inputs for each particular job.

I hope this helps until more documentation is available.

Cheers,
Kye

3

Thanks Kye! This was exactly what I was looking for. I hope the cryosparc devs continue to add features which support automated workflows.

4

I second @kyestachowski’s suggestion of looking at job-specific build.py files, as well as your own of referring to job.json files’ respective params_base sections.

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