Batch processing and command line tryphoncosinus  2023-02-08 14:39

Dear team,

Quite new with Skyline. I would like to run DIA analysis with quite large set of MS data. The idea:

  • Prepare analysis configuration/libraries using Skyline and Skyline batch programs under a standard Windows machine.
  • Execute this configuration on a powerful server using only the command line through Skyline.exe / SkylineBatch.exe, i.e., without any graphic UI that is not available on this machine (I checked I can execute SkylineCmd.exe --help on it).
  • Go back with result files on the standard machine for Skyline visualization.

Is there any way to achieve this idea or alike and process the workflow with no more user intervention? Or suggestions ?

Thank you for your help.

Nick Shulman responded:  2023-02-08 16:42
Yes, it should be possible to get Skyline to run on another computer as you describe.
Skyline usually gets installed in the user's home directory by the web installer.
You might find it easier if Skyline gets installed in the C:\Program Files folder, in which case you should use the "Skyline Administrator Install":

The conventional way to drive Skyline is by writing a Windows batch file which invokes SkylineRunner.exe (if you don't know where Skyline is installed) or SkylineCmd.exe (if you know which folder Skyline is installed in).
You might want to use Skyline Batch instead of writing a batch file:

The place to get the most up-to-date documentation about the Skyline command line interface is with the menu item "Help > Documentation > Command Line". (Actually, I guess "SkylineCmd.exe --help" is a different way to see the same information).

Let us know if you run into any problems.
-- Nick
tryphoncosinus responded:  2023-02-09 16:26
This sounds tasty. I started to look and read.

Thank you Nick.