Hi Amin,
We have not written one yet, but you can find the reference (and SkylineRunner.exe) on the page below where you installed from and also here:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=documentation

And you might start with the DIA webinars from last year:

https://skyline.ms/webinar14.url
https://skyline.ms/webinar15.url

Which make use of the SkylineRunner command-line interface and provide some useful batch scripts and show how to connect R post-processing of Skyline reports. I find I have used these batch scripts a lot as a starting point for running Skyline command-line processing.

Hope this helps. Sorry we don't have exactly what you are looking for.

--Brendan

Thanks Brenden for the information. I will look into these webinar.

Also is there a way to install skyline in a specific folder. Currently it installs in the apps directory under some folder generated with a arbitrary name.

   Amin

Hi Amin,
You can always just download the "unplugged" installation, which comes in a ZIP file. That ZIP file contains a setup.exe, which will also install to the apps directory, but you can just ignore that and run Skyline.exe from wherever you put it on the disk drive. Everything you need is contained in the extracted folder.

If you do this, however, you will not get the Windows Explorer file association and SkylineRunner.exe will not be able to find this version of Skyline.exe. Instead, when you have simply extracted all the files to a folder, you should run SkylineCmd.exe as your command-line entry point.

This has become a preferred mechanism for setting up and testing pipelines involving the Skyline command-line interface. It sure has made iterative development and debugging of the command-line easier, since we no longer need to involve SkylineRunner.exe and an installation of Skyline to the apps folder.

Thanks for your interest in the Skyline command-line interface and probing into what it can provide.

--Brendan