How to add a custom workflow?

Features and Functionality
5

Hi @rkhayat, we don’t yet have a way to do this in the cryoSPARC interface. However, if you’re willing to write some Python code then you can set this up with cryoSPARC’s interactive CLI.

First check out the Python code for the Extensive Workflow at /path/to/cryosparc_master/cryosparc_compute/jobs/workflows/buildrun_bench.py

Look for the run_extensive_workflow(job) function. It’s code automatically queues and runs all the jobs for the T20S Tutorial. You may use snippets from this code directly in cryoSPARC’s interactive CLI mode (the cryosparcm icli shell command):

$ cryosparcm icli
Python 2.7.15 |Anaconda, Inc.| (default, Oct 10 2018, 21:32:13) 
Type "copyright", "credits" or "license" for more information.

IPython 5.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.
^[[A
 connecting to cryosparc:39002 ...
 cli, rtp, db, gfs and tools ready to use

In [1]: puid = 'P2'  # Substitute with your project ID
   ...: wuid = 'W1'  # Substitute with your workspace ID
   ...: uuid = db.users.find_one({'name': 'YOUR NAME'})['_id'] # Substitute with your cryoSPARC user name
   ...: 

In [2]: movies_juid = cli.make_job(
   ...:     job_type='import_movies',
   ...:     project_uid=puid,
   ...:     workspace_uid=wuid,
   ...:     user_id=uuid,
   ...:     params={ # Substitute each parameter with your dataset parameters
   ...:         'blob_paths': '/path/to/movies/*.tif',
   ...:         'gainref_path': '/path/to/movies/gainref.mrc',
   ...:         'psize_A': 0.6575,
   ...:         'accel_kv': 300,
   ...:         'cs_mm': 2.7,
   ...:         'total_dose_e_per_A2': 53
   ...:     }
   ...: )

In [3]: cli.enqueue_job(puid, movies_juid, 'default')  # Substitute last arg with a worker lane name
Out[3]: u'launched'

In [4]:

The code also shows examples for connecting job inputs and even interacting with Interactive jobs.

Hope that helps, let me know if you run into trouble with any of that!

Nick

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