This is a suggestion from Dr. Steve Chervitz of Personalis in Menlo Park.
Fix ftp quickload
Add blacklist regions to IGB quickload for mouse, human, fruit fly
Update GIAB annots.xml to point to S3
GIAB data sets feature several highly sequenced individuals/families. Each individual has sequencing from different technologies, such as Illumina, Oxford Nanopore, and PacBio, making it a rich source of different data types that are comparable.
A tag is merely a pointer to a specific commit. I'm not sure that you can re-attach it to a different commit after the fact. So I'm not sure how this will work....
I have created a pull request with the changes to igbDefaultPrefs.json here:
To make the mirror I created a github repository and used the instructions here to create a git mirror.
git clone --mirror https://github.com/exampleuser/repository-to-mirror.git
git remote set-url --push origin https://github.com/exampleuser/mirrored
git fetch -p origin
git push --mirror
PR is merged into IGB code base.
Moved to complete. Thank you Nowlan Freese!
If there are additional tasks to be done (???), let's make new Jira issue for them.
Tested on 9.1.8 jar with no issues.