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Executing Skyline GUI with a .sky file already loaded

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Executing Skyline GUI with a .sky file already loaded sdelacam  2025-12-18 02:17
 

Dear Skyline team,

My name is Samuel and I am currently developing a software for Quality control in my core facility. It is a streamlit application developed in python which actually detects when a ".raw" file is generated in my directory and automatically launches skyline. For that purpose a template is taken into account for searching albumin. Everything works correctly, my ".raw" files are automatically searched and results are stored with the information I seek but my problem arises when I try to launch the skyline GUI with the ".sky" file result I want to inspect. I manage to launch the skyline GUI but not with the .sky file loaded.

Could I achieve to executethe Skyline GUI with my .sky file loaded?. Here I attach the "launch_skyline.bat" script which is set to launch the GUI.

Kind regards,
Samuel
 
 
Brendan MacLean responded:  2025-12-21 22:01

Hi Samuel,

To launch Skyline GUI with a document already loaded, simply pass the .sky file path as an argument:

"C:\Program Files\Skyline\Skyline.exe" "C:\path\to\your\results.sky"

Make sure to quote both paths if they contain spaces.

Reading your batch file, you are confusing Skyline.exe (the GUI) and SkylineCmd.exe (the CLI). They are separate processes that do not talk to each other. You can get an open file in the GUI, as described above.

Your batch script does the following:

  1. Open Skyline with no extra information.
  2. Run the CLI using a specific file, but because you don't ask it to do anything else, SkylineCmd simply opens (with no connection to any UI) loads the specified Skyline document (.sky file) and then ends the process without doing any meaningful work.

It seems like you have found the CLI documentation in either Help > Documentation > Command-Line or on the website:

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

Finally, Skyline should install with an association with the .sky extension, if this gets broken, there is a Tip on how to fix it in the Windows registry:

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

When that is correctly registered you should be able to double-click on .sky files; they should show up in Windows File Explorer with a Skyline icon, and you should simply be able to use:

start MyFavorite.sky

On the command-line or in a batch file.

Thanks for posting to the Skyline support board. I hope this information helps.

--Brendan
 
Nick Shulman responded:  2025-12-21 22:35
Actually, in order to bring up the Skyline GUI, the first command-line argument has to be "--opendoc" because otherwise Skyline.exe thinks you are trying to invoke a command-line command.

So, it would be:
"C:\Program Files\Skyline\Skyline.exe" --opendoc "C:\path\to\your\results.sky"

(It might be that we should change things so that "Skyline.exe" act like the command-line version when it sees arguments on the command-line which would make the "--opendoc" argument unnecessary.)