Scaffold Batch Cheat Sheet

scaffold.md

Scaffold Batch Howto

If your scaffold run is longer than an hour or so its a good idea to run it in batch mode. This allows others to run the scaffold GUI at the same time and will run in the background until done.

1. Setup your scaffold run using the GUI but dont actually start the run
2. Save your scaffold file using the save as dialog (eg myrun.sf3)
3. Choose Export -> Scaffold Batch and save your batch file (eg myrun.scafml )
4. Open the Windows Powershell program. This should give a command prompt

Powershell Commands

First navigate to the folder where your scafml file is located. For example if your file is located on the F drive under the Serum folder you would do

  F:
  cd .\Serum

Then check that your file is present. For example if your file was myrun.scafml you would type the following from the Serum directory

  ls myrun.scafml

If you get an error it will probably be because your file isn't present or because you mistyped its name. Double check your typing as even a tiny mistake will cause the commands to fail. If the above command worked it means you are in the right directory and the file has the name you expect. Now start scaffold with the magic command

   & 'C:\Program Files\Scaffold 4\ScaffoldBatch4.exe' -f F:\Serum\myrun.scafml

Scaffold should now start spewing heaps of text to the screen. This is normal. Every dozen lines or so it will show a percentage complete number. When it's done you it will update the myrun.sf3 file to contain the final results. If you want to abort at any time just press Ctrl-C