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cianfrocco-lab / COSMIC-CryoEM-Gateway

Web platform for analyzing cryo-EM data on Comet cluster at San Diego Supercomputer Center
http://cosmic-cryoem.org
GNU General Public License v3.0
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'Ingest' data into data page after job finishes #152

Open mcianfrocco opened 5 years ago

mcianfrocco commented 5 years ago

Hi @monaw - as the gateway currently exists, we wrote it such that when 2D and 3D analysis routines finish, the data does not repopulate into the 'Data' page. This setup is still OK for now.

In talking with potential users informally, I am considering to add upstream commands for the gateway, allowing more preprocessing of the data via COSMIC2.

Short version: As such, I'm wondering, is there a way that certain jobs can have their output star files listed into the 'Data' page for a given Folder on the gateway?

Long version: Right now, we take particle stacks as inputs for 2D / 3D analysis. I'm wondering if we can offer upstream steps that allow users to run automatic particle selection from micrographs, where the input are micrographs and the output is a particle stack. In this type of job, I would like to be able to take the output from this step (a particle stack in .star file format as we already are used to) and list it in the data page.

What do you think about feasibility ?

Mike

monaw commented 5 years ago

@mcianfrocco - you mentioned "certain jobs" above...so how will these jobs be determined? by the user or another mean?

mcianfrocco commented 5 years ago

"Certain jobs" right now is the "Preprocessing" tool. The output of preprocessing is a particle stack that could be used directly in 2D and 3D analysis