Skyline batch installation and use

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Skyline batch installation and use j3 menzel  2021-04-18
 

Dear Skyline team,

I often run a small molecule analysis workflow using between 40000 up to 900000 transitions and exporting results with a report template. Both reading transition lists and datasets takes a long time, so I wanted to try Skyline batch to increase the speed of getting to the report file (as I have no need to look at or manipulate results manually in Skyline in this step).

When I downloaded Skyline batch I couldn't see all the parts of the menu (in Skyline batch configuration: Files, Refine) and I couldn't run the analysis of the dataset as the process exited before saving an output file.

Once I downloaded the latest version of Skyline Batch, installation (initialization) simply fails (on various computers), despite the latest Skyline version being installed.

Could someone help me or point me towards a site with more options?

Thanks for the great support,

Philipp

 
 
Brendan MacLean responded:  2021-04-18

Please provide screenshots or log files of the failure you are seeing.

Skyline Batch supports a somewhat limited set of workflows. Your most flexible option is still to write your own command line batch file to run SkylineRunner or SkylineCmd.

Have you looked through the tutorials and companion webinars to understand what it can do? For instance, it currently expects you to provide a template Skyline document with all your settings into which you will import raw data files. It does not support any method to import targets (e.g. transition lists) into a targetless document with only settings as you seem to be hoping for.

Hope we can help you mor to make use of this powerful new tool. Though, for now, you likely have to adapt your expectations to what it can actually do, and then request what more you might hope for.

Of course, it should not crash on initialization.

—Brendan

 
j3 menzel responded:  2021-04-18

Hi Brendan,

thank you so much for the quick response!

I have attached here the error message and the log file that the error message refers to.
Could re-installing Skyline itself and then trying to reinstall Skyline batch possibly help?

I have all settings files ready including a skyline template file, which already has a transition list loaded. As a first step I would be very happy if I could install and test Skyline Batch in the simplest way of applying it.

Apart from that, is there a resource to access an example command line batch file with SkylineRunner or SkylineCmd?
It would be great to see one working example from which to learn to modify to my own needs and data. I will continue looking through the webinars to get more information on SkylineRunner and Cmd.

Thanks for your support,

Philipp

 
Brendan MacLean responded:  2021-04-18

Skyline Batch should be pretty independent from Skyline. First try completely uninstalling Skyline Batch and then reinstalling it. This appears to be and incompatibility between a saved configuration from and older versions. Skyline Batch still being fairly new, we have preferred improving it quickly over maintaining perfect backward compatibility with older versions. This means you may have to uninstall and reinstall to clear out old incompatible settings.

Thanks for providing the details. I have run into this myself testing, but we figured the number of people using it is still likely very small.

—Brendan

 
j3 menzel responded:  2021-04-18

Hi Brendan,

thanks a lot.
I can now run Skyline Batch and generate the output that I was hoping for.

Cheers,
Philipp