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Requirements
Synapse account
Python 3.7+
(for local testing) CWL runner of choice, e.g. cwltool
Access to cloud compute services, e.g. AWS, GCP, etc.
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3. Update the quota of the Evaluation queue, such as the Duration (Round Start, Round End) and Submission Limits. Generally, there are no submission limits for write-ups, so that field can be left blank.
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Get the 7-digit Evaluation ID as it will later be needed in Step 9. |
4. Go to the Sage Bionetworks Challenges repo group, and create a New repo.
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7. In the pop-up window, switch tabs to Link to URL. For "URL", you will need to provide the link enter the web address to the zipped archive download of the write-up workflow infrastructure repository. You can may get this link address by going back to the repo, repository and clicking on Code, then > right-clicking on Download ZIPZip > Copy Link Address. Give the File Link any Name you’d like, :
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Name the file (e.g. "writeup-workflow8. Click on File Tools > Annotations. Click on Edit and add an annotation called ROOT_TEMPLATE. For “Value”, enter "), then click Save.
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This file will be what links the evaluation queue to the orchestrator. Make note of this File ID for use later in Step 9. |
8. Add an annotation to the file called ROOT_TEMPLATE by clicking on the annotations icon:
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The “Value” will be the path to the workflow script, written as:
{infrastructure workflow repo}-{branch}/{path/to/workflow.cwl}
For example:
my-writeup-repo-main/workflow.cwl
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Feel free to look at the other infrastructure files to see how the ROOT_TEMPLATE annotations are written.
9.
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9. There are two approaches for running the writeup workflow. You can either:
a) tack on the evaluation + workflow onto an existing instance with Orchestrator, by adding another key-value pair to EVALUATION_TEMPLATES
b) create a new instance (a t3.small would be sufficient enough) and setup Orchestrator on that machine. See Steps 7-9, 11 of Creating and Managing a Challenge for more details on how to set this up.