Any plans for a Linux version of Skyline (even with limited capabilities)?

Any plans for a Linux version of Skyline (even with limited capabilities)? lparsons  2017-08-07
Skyline is a great tool for me, and I am wondering if there are any plans to make it available - even in a somewhat stripped-down form - for Linux. I have read that the vendor specific libraries that make it possible to open vendor native formats are often locked to Windows, but there are other functions that could be helpful to have that might not require them. If I could open an existing Skyline project and do basic editing of the project (for example deleting ions) and basic exporting (to text) that would be really helpful for me.
I don't know the ins and outs of the Skyline .sky file format (amongst other things), so I don't know if that is a request that would be too great to handle or not.

thank you!
Brendan MacLean responded:  2017-08-07
Hi Lee,
There are no plans to port the UI to Linux. We very much hope we will be able to have a Linux command-line only option for running large-scale processing work on a cluster or "in the cloud". As you indicate, even that is likely to have limited access to instrument vendor formats and often require converting them to a standard format (on a Windows computer) like mzML, mzXML or mz5 before they can be processed on Linux.

That effort will be big enough. You shouldn't expect to see the Skyline UI even in a limited form running on any non-Windows system.

Thanks for posting your question to the Skyline support board.

jmeyer responded:  2018-11-12
Dear Brendan,

Curious if you have any update on this command-line only option for processing on linux clusters?

Matt Chambers responded:  2018-11-12
Hi Jesse,

Great news on this front. You can run msconvert and SkylineCmd via a Docker container. I haven't yet started automatically updated the container on DockerHub, but you can download the container from:

Then you can run 'docker load' on that tarball. Then follow the instructions here:

Instead of chambm/pwiz-skyline-i-agree-to-the-vendor-licenses, use whatever image name you loaded from the tarball above. Also, 'SkylineCmd help' doesn't actually output any help information. Refer to the documentation instead:
Brendan MacLean responded:  2019-04-25
It seems an update is in order. The DockerHub location has changed to (or well both work at the moment):

Also, the command:

SkylineCmd --help

Now works as expected producing output that looks a lot like the DOCX file Matt mentioned, but it is guaranteed to be the most up-to-date command-line documentation, which you can also get in an HTML formatted table in the Skyline-daily UI through Help > Documentation > Command Line.

We have been using this version successfully on Linux under AWS EC2 for our own pipeline implementation coming soon on
dsullivan responded:  2021-09-13
Hi Brendan,

I have been using the linked docker image to run skyline on linux and it had been working quite well until recently. I somehow broke my build, so I figured I might as well download an updated version of the docker image as my current tag was a year or more old.

Upon a brief search I found that "Running Skyline on docker is possible but it is no longer maintained." ( While I understand the complexities of maintaining the docker build, is there an alternative to getting an up-to-date instance of skyline running on our linux servers?

I can of course use an outdated skyline/docker container, but for reasons similar to those outlined in the linked article, that becomes difficult when the system does not perform as expected.

Any assistance getting the latest version of skyline running in a linux environment would be greatly appreciated.

Matt Chambers responded:  2021-09-13

Hah, that's the wrong Skyline:

Skyline is a real time anomaly detection, time series analysis and performance monitoring system, built to enable passive monitoring on metrics, without the need to configure a model/thresholds for each one. It is designed to be used wherever there are a large quantity of high-resolution time series which need constant monitoring. Once a metrics stream is set up additional metrics are automatically added to Skyline for analysis. Skyline's algorithms attempt to automatically detect what it means for each metric to be anomalous. Once set up and running, Skyline allows the user to train it what is not anomalous on a per metric basis.

The ProteoWizard/Skyline image is still officially maintained:

Matt Chambers responded:  2021-09-13

It sounds like AutoQC could feed data into either Skyline though. Wouldn't that be confusing? :)

dsullivan responded:  2021-09-13

Hah, well I feel silly! Good to know that the docker image is still being supported!!!

I will try the most recent version. And yes, that would be very confusing. :)

Thanks again!