Using variables within config.toml files

[phillip.a...@gmail.com]

Hello,

I was wondering what the syntax is for using variables within TOML format config files. I first looked here (https://github.com/toml-lang/toml), but didn't find anything. 

The reason I'm looking, is that when I'm using multiple systems I'd like to be able to just change a single line in the config files. Something similar to bash scripting:

DATABASE_DIR=/some/perfect/location/

# FATHMM-XF Noncoding

[[annotation]]

file = "${DATABASE_DIR}/fathmm_xf_noncoding.vcf.gz"

columns = [5]

names = ["FATHMM-XF"]

ops = ["self"]

 

I guess it's not the end of the world if it isn't possible but I figured I'd ask before writing a wrapper.

Cheers,

Phil

[Brent Pedersen]

Hi Phil,
this isn't possible right now. I guess I could expand user vars in
file paths, but they'd have to be specified outside of the file.

vcfanno does have the -d option so you can specify a base-path for all
the files.

that said, if you'd open an issue on the vcfanno repo, I'll consider
expanding user variables defined in the environment in the `file`
values.

-Brent

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