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alliance-genome / agr_file_generator

This repo is for generating files from Alliance resources
MIT License
1 stars 3 forks source link

adding tabix files to VCF generation #AGR-2323 #106

Closed adamjohnwright closed 4 years ago

adamjohnwright commented 4 years ago

@scottcain once this is pulled in you can start using the index files whenever you like with your VCF JBrowse pipeline.

@paaatrick also after this is pulled in do you mind adding a TBI button to the Downloads page for 3.2 - build?

paaatrick commented 4 years ago

I'd be happy to. Can you open a jira issue with the relevant information (file types and subtypes, which section to add them to, etc) and assign it to me?

adamjohnwright commented 4 years ago

@paaatrick @zfinannee just let me know that Sabrina would like to have adding it to the Downloads page discussed on the Friday call. So I guess there is no final decision for now. If we decide to move forward with it I can create another ticket for the UI work.

adamjohnwright commented 4 years ago

@oblodgett I think I wrote it above. But if you feel like they should be in the base image please feel free to add those two packages. I am not sure what the full process is of making them available. I know you like to create the new base images a the beginning of releases. I am not sure if add these in could risk changing the containers on the staging machine etc.. Just let me know when the packages have been installed and I will remove them from this repos Dockerfile.

oblodgett commented 4 years ago

If you look in the base image https://github.com/alliance-genome/agr_base_linux_env/blob/master/Dockerfile you would see that it is installed already, tabix that is, but vcftools would need to be added.