Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clarify the purpose/use of the release number in ensembl_info.py #1248

Open
grahamgower opened this issue May 14, 2022 · 1 comment
Open

Comments

@grahamgower
Copy link
Member

grahamgower commented May 14, 2022

stdpopsim/catalog/ensembl_info.py currently shows the release number to be 103. This implies all species are at this release number. It also implies that when a new species is added, it should come from that same release. But our maintenance code doesn't support this---instead the new species will come from the most recent ensembl release, and the maintenance code will bump the release number. So now different species correspond to different release numbers. What number should be in ensembl_info.py?

Clearly we should not require that when a new species is added that all existing species get updated (in particular because an update can require recombination map liftover).

@jeromekelleher
Copy link
Member

Clearly we should not require that when a new species is added that all existing species get updated (in particular because an update can require recombination map liftover).

You're right, the release number should be moved into the species data I guess. I had envisaged that we would periodically update the whole catalog to reflect the most recent data from Ensembl, but I hadn't imagined we were going to add this many species.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants