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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
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How to access Jasix #126

Closed vajanishant closed 4 months ago

vajanishant commented 4 months ago

Hello guys,

I was trying to run this: sudo docker run --rm -it -v Data:/scratch annotation/nirvana:3.14 dotnet bin/Release/net6.0/Jasix.dll -i dragen.json.gz -q chr1:942450-942455

But it is throwing an error: 

Did you mean to run dotnet SDK commands? Please install dotnet SDK from:
  https://go.microsoft.com/fwlink/?LinkID=798306&clcid=0x409

I also generated a file json and jsi files: HiSeq.json.gz.jsi, HiSeq.json.gz

But how can I access HiSeq.json.gz.jsi this file? There's not way to convert this to json or something that should be visible in human readable format?

I'm using gitpod to execute Nirvana via docker.

Distributor ID: Ubuntu
Description:    Ubuntu 22.04.4 LTS
Release:    22.04
Codename:   jammy

I've installed dotnet: 

sudo apt-get update &&   sudo apt-get install -y dotnet-sdk-6.0
dotnet --version
6.0.127

Please guide me here so that I can get the jsi file in json format or can be able to generate Jasix and can read it in human readable format.

Thanks in advance.

rajatshuvro commented 4 months ago

Hi @vajanishant , Unfortunately, Nirvana is no longer public. Please follow the instructions here https://illumina.github.io/NirvanaDocumentation/ to get the latest version.

Best Rajat