VIP processing through Shanoir
VIP (https://vip.creatis.insa-lyon.fr/) is a web portal for medical imaging applications. It allows access to scientific applications as a service, as well as distributed computing resources available in the biomed virtual organization of the EGI e-infrastructure.
Shanoir allow an authenticated user to start executions on VIP platform
To access VIP pipelines and start execution from Shanoir, the authenticated user must have previously created an account on the VIP platform.
This user must have the same email address than the Shanoir account, so that the 2 account can be linked between the two application.
To create an account on VIP, see https://vip.creatis.insa-lyon.fr/sign-up.html.
Dataset to process through VIP pipeline are selected through the Dataset search (Solr) view.
Once the selection made, click the Run a process button. The user must have admin rights on all the selected datasets.
The user can then select one of the VIP pipelines he has access to. Click Run this pipeline` button to configure the pipeline execution.
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Execution nameis filled by default but can me modified by the user Group byDataset export format
Other fields are execution parameters, specific to the chosen pipeline.
infile type fields correspond to the selected datasets. User can alter their selection by using regular expressions in these fields.
Once the execution started (after a few seconds), the user is redirected to the Details on dataset processing view.
The user can follow the state of the execution through the Jobs view.
In the Details on dataset processing view, he can check the status of the execution, and download some logs from VIP.
At the end of a successful execution, processings and processed datasets are created under each selected datasets.
The processings represents the VIP pipeline execution.
The processed dataset contains the raw results archive of the VIP execution, that can be downloaded through the Download process data button in the Details on dataset view
Some pipelines (e.g. ofsep_sequence_identification) can trigger specifically developed post-processing.