lua flag error!

[alka...@gmail.com]

Hi Brent,

Thank you again for the great tools that make gemini the best one-stop annotation software.

I tried to run the "gem.conf" in the examples folder of github to do the full gemini annotation after adding my own scripts of [[annotation]] for my vcf and bed files.

Whenever I run the vcfanno as follows:

$vcfanno gem.conf my.vcf > annotated.vcf

I get the following message:

"vcfanno.go:95: ERROR: requested lua op without specifying -lua flag"

I tried to add the '-lua' flag as:

$vcfanno -lua gem.conf my.vcf > annotated.vcf

or changing the extension from '.conf' to '.toml' 

$vcfanno gem.toml my.vcf > annotated.vcf

But I still couldn't get it successfully run. I couldn't find any lua extension file in the examples folder, except for the clinvar one.

Do I have to write a lua file together with the .conf ('.toml') file to run it?

Best regards,

Ahmed

[Brent Pedersen]

Hi Ahmed, glad you're finding the tools useful. You can do

vcfanno -lua <(echo "") gem.conf my.vcf

or just give it an empty file. but if you're using the gem.conf from
the repo, you'll need:

vcfanno -lua custom.lua gem.conf my.vcf

where custom.lua is in the examples/ directory next to gem.conf.

hope that helps,
-Brent

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[alka...@gmail.com]

Thanks a lot for the quick and detailed response Brent!

I was able to get rid of that error message, and now in the phase of refining my configuration script, and annotation files.

Warmest regards,

Ahmed