When a pydpiper pipeline has been completed and the results are ready to go into our ScanBase database or OBI's brainCODE database you will need to upload your results into the ScanBase googlesheet.To simplify this process there is an R package "scanbaseTools" installed on the system that allows you to upload easily.
- You are required to prepare some metadata before you can begin uploading. Presently the metadata consists of 4 small csvs. This is where you give all the details needed to understand the study. Please try to be as complete as possible with the metadata.
Individual scan metadata: example_scan_sheet_setd5.csv
Genotypes used in the study:example_genotypes_sheet_setd5.csv
Treatments used in the study:example_treatments_sheet_setd5.csv
These files should be up to date, but to be sure you can also use the versions found in scanbaseTools by running
- Be prepared for a long running command. Possibly sign in and do this on HPF (whoops, not yet, the required version of minc-stuffs isn't installed there yet).
- scanbaseTools will prompt you to log in to googlesheets, you'll need to use the account firstname.lastname@example.org, password available from me and Jacob on request.
- Be patient.
- ScanbaseTools will attempt to upload the data to google sheets.
- Check that the upload occurred successfully by inspecting test_scanbase_40um on googlesheets.
- If you were unable to upload and the command fails, don't fret, just run the `upload_study` command again. It should be much much faster the second time.
- Once we've all determined that the uploads are working properly, I'll switch the default to upload to scanbase_40um (not the test version).