How do I create skyline file (.sky file) using command line

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How do I create skyline file (.sky file) using command line Bhoomi Dhananjay Bhatt  2018-02-05 13:14
 
E:\Skyline-64_4_1_0_11714\SkylineRunner.exe --in="C:\Users\shiro\Documents\TargetedMSMS_2\Low Res\test1.sky" -import-fasta=E:\prm\9606_refseq_2017_11_29.fa --import-all=E:\core\ --exp-translist-instrument=Thermo --exp-file=E:\core\test1.tab

Here, test1.sky was created using skyline GUI prior to running this line of code.

Thanks,
Bhoomi
 
 
Brendan MacLean responded:  2018-02-05 14:15
—save to save in place or —out=path/to/file.sky to save to a new location. Though, these are the second and third arguments in the documentation. So, maybe I am missing what you are looking for, since you have obviously started using SkylineRunner.

Does this help? If not, please clarify.

—Brendan
 
Bhoomi Dhananjay Bhatt responded:  2018-02-05 14:34
I just want to create a new .sky file. for the --in=file.sky, the sky file needs to exist. How do I make this file?
 
Brendan MacLean responded:  2018-02-05 20:28
What would you do next? We offer very limited ability to edit your settings through the command-line. Are you expecting to start with our default settings? The best way to start with some predefined settings is to set them up and then save them in a .sky file. Then you would put that somewhere as your template document (no targets necessary) use --in to open it and --out to put your modified version anywhere you want.

So, imagine I implemented a --new for you that allowed you to start with an empty Skyline document and our default settings. What would you do next?

Still not clear on why this would be better than --in and a template Skyline document. Even if you really want to start with our default settings. Just use File > New and then Settings > Default, and save that to Default.sky, and then use --in=path/to/Default.sky

Just not seeing what we are keeping you from doing. Please clarify.

--Brendan
 
Bhoomi Dhananjay Bhatt responded:  2018-02-06 08:00
I want to create a template using command line rather than going to the GUI every time so yes I want to start with the default setting from command line itself.
 
Brendan MacLean responded:  2018-02-07 00:52
So, does saving a Default.sky file and opening it work for you?

This is equivalent to File > New and then Settings > Default, or vice versa. And, of course, the same strategy allows you to create any number of (target-free) template documents you like and start from them.

--Brendan