Saving file to older version of skyline

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Saving file to older version of skyline dsullivan  2019-09-09
 

Hi all,

I am currently using the docker image for running Proteowizard/Skyline developed (https://hub.docker.com/r/proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses)

It's great! Thanks!

Recently Skyline updated to version 19, and this has sadly broken the pipeline since skyline 4.2 cannot open the blank .sky files necessary for running a job in skyline. Is there any way to save a .sky file with an old version tag? (and/or update the docker image)

Regards,
Devin

 
 
Nick Shulman responded:  2019-09-09
Devin,

In Skyline, you can use the menu item:
File > Share
to save the document in the format of an older version of Skyline.

(I don't know anything about updating the Docker image).
-- Nick
 
dsullivan responded:  2019-09-09
Hi Nick,

Thanks for the fast reply. I am able to export the file using that function without error, but I don't seem to be able to read it.

When trying to read with skyline 19.1 (which was used for export) I get:
---------------------------
Skyline
---------------------------
Failure opening C:\Users\Devin\my_dummy_4_2.sky.
The file you are trying to open ("C:\Users\Devin\my_dummy_4_2.sky") does not appear to be a Skyline document. Skyline documents normally have a ".sky" or ".sky.zip" filename extension and are in XML format.
---------------------------
OK More Info
---------------------------
System.IO.IOException: The file you are trying to open ("C:\Users\Devin\my_dummy_4_2.sky") does not appear to be a Skyline document. Skyline documents normally have a ".sky" or ".sky.zip" filename extension and are in XML format.
---------------------------

Failure opening C:\Users\Devin\my_dummy_4_2.sky

///////////////////////////////////////////////////

When trying to read with the dockerized skyline v4.2 I get:
The file contains an error on line 1 at column 1.

Any thoughts?

Regards,
Devin
 
Nick Shulman responded:  2019-09-09
Devin,

When you do "File > Share", Skyline creates a .zip file. Those files are normally saved with the extension ".sky.zip".
It sounds like you might have forced the file to be saved with the ".sky" filename extension.
If you rename the file to something that ends in ".zip" you will probably be able to open it in Skyline.
Also, after you fix the filename extension you can use Windows Explorer to see the files in the .zip file. You can use Windows Explorer to copy the .sky file out of the .zip.
-- Nick
 
dsullivan responded:  2019-09-09
Hi Nick,

I did not force it to save as .sky, however when I forced the file extension to .sky.zip skyline 19 *could* open it. So it appears there is a small but manageable bug there.

I still can't get skyline 4.2 to open it however as I receive the same error message as before:
Success! Imported Reports from Precursor_analysis
Opening file...
Error: There was an error opening the file Z:\code\my_dummy_4_2_c.sky.zip
The file contains an error on line 1 at column 1.
Exiting...

Is there a download link for skyline 4.2 so I can install that and see if the issue is indeed with skyline 4.2 or the dockerized version of skyline.

Regards,
Devin
 
Brendan MacLean responded:  2019-09-09
Here Skyline is expecting a .sky file. I don't think it can deal with a .sky.zip file. You will need to unzip the .sky.zip file and point SkylineCmd at the .sky file inside.
 
dsullivan responded:  2019-09-09
Hi Brendan,

Thanks for the input. That worked!

So the procedure is this:
1. Edit file in v19.1
2. Save file in v19.1
3. File > Share > v4.2 -- this will create a file that is .sky but should be .sky.zip (see step 4) and as a result cannot be opened by v19.1 or v4.2
4. Rename file (using powershell or terminal, not GUI) to end in .sky.zip -- This will now open in v19.1 but NOT v4.2
5. unzip the file with whatever tool you want...This will extract a file with the name of the file you saved in 19.1 (not the name you saved which is the zip file). -- this will open in v4.2!!!
6. Run your favorite skyline v4.2 script (in my case the docker image).
7. Thank Brendan, Nick and the whole Skyline team!

-Devin
 
Brendan MacLean responded:  2019-09-09
Hi Devin,
My expectation would be:
1. Edit file in v19.1
3. From 19.1 File > Share > v4.2 (which causes a save of the document) -- this will create a file that is .sky.zip (maybe check that your Windows Explorer is showing file extensions, or you may mistakenly think it does not end in .zip)
4. This .sky.zip file can be opened in the Skyline user interface by either 19.1 or 4.2, using File > Open. When you open the file in the user interface it will be extracted to a folder with the base name.
5. Or you can unzip the file with whatever tool you want...This will extract a file with the name of the file you saved in 19.1 (not the name you saved which is the zip file)
6. Once you have the .sky file unzipped in a folder, then you can use the Docker Container SkylineCmd for 4.2 to open it from the command-line.
7. Run your favorite skyline v4.2 script (in my case the docker image).

I think in your own description, the terminology "Open" means using the command-line, and not the user interface. The user interface can open these files using File > Open. It is just the command-line which has problems with .sky.zip files. I also think the whole renaming the file thing was a mistake, based on the way you were using "Open". Nick, mistakenly thought you mean File > Open when you really meant open with the command-line, which assumes you are giving it an uncompressed .sky file no matter what.

Anyway. Confusing, but glad to hear you have something working. I think if you continue to explore, you will find it is not as complicated as the steps you have outlined, and you will eventually land on a more optimal route to achieving what you are looking for.

--Brendan