[scipion-users] Cleaning workspaces

[Christian T. <chr...@bi...>]

Hi Scipion Team,

I have a few questions regarding project cleaning and space usage.

(a) "clean" the data of a job, but keep the settings.
This is mainly for particle extraction jobs. These are often the jobs, that requires the most space, but the job in principle could be redo at any time, as you just need coordinates and box-size. In cryoSPARC, one can easily clean a job by "Clear Job", which deletes all the generated files, but keep the settings. Is something similar possible in scipion as well?

(b) identify redundant and obsolete jobs. 

Often multiple rounds of picking, extracting and 2D classification are done to get a good subset of particles. But the initial jobs, useful in the beginning, are often not needed for the later refinements. Is there a way of identifying jobs, that are potentially obsolete? Again, deleting them would be over the top, but cleaning these data as questioned in (a). Also, if a project is challenging, one might run multiple parallel jobs eventually creating redundancy, which blocks also space. Is there a easy way of analysing the workflow tree? I saw that there are some sqlite databases in the project folders, but it was not clear for me, how I can extract the tree from there, to see, if there are multiple/redundant jobs. 


(c) Identify dead-end forks.
This goes hand-in-hand with (b). Is there a easy way of getting the entire tree from the project folder/database, to analyse it independently? Like getting the node information and use some python code, to get the information, without using the scipion gui (which is a bit laggy over ssh and x-forwarding).

Best
Christian