sgkit
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sgkit-dev
Scalable genetics toolkit
Add a GitHub action to deploy the docs for a new release when the release is made. The manual instructions are here: https://github.com/pystatgen/sgkit/issues/608#issuecomment-891117795. We might also look at tskit's automation...
@tomwhite wrote up some great instructions at https://github.com/pystatgen/sgkit/issues/608#issuecomment-891117795. We should probably put these instructions somewhere more permanent, though I'm not quite sure where. Perhaps as a discussion at https://github.com/orgs/pystatgen/teams/committers?
It will add complexity to our doc build and push but I think we're at the point now where we should support searching different versions of the docs, including the...
Before posting this issue I searched the entire StackExchange universe and Biostars for questions about this package and there were none. So I decided I would get any help on...
Here is some results of Allele Frequency's distributed benchmark on 1000 Genome data: I set up the experiment with [1,2,4,8] machines, data are stored in HDFS running on the nodes...
It seems like the GPU tests have started to fail with the latest Numba version: Ref: https://github.com/pystatgen/sgkit/runs/4906151881?check_suite_focus=true ``` self = dispatcher = griddim = (1, 1, 1), blockdim = (32,...
I have set up HDFS and can store(hdfs dfs -put) data to it, read dataset for Sgkit using `load_dataset("hdfs://node0:9000/chr21.zarr")`, but it seems that I cannot write the output or say...
sgkit stores genomic windows as the indices of their first and last variants within each window. This means that filtering variants (i.e. dropping some variants from the dataset) will invalidate...
Algolia has changed the DocSearch program and it's going to require some code changes on our side. [Gmail - Fwd_ The DocSearch team have some exciting news for you!.pdf](https://github.com/pystatgen/sgkit/files/7785120/Gmail.-.Fwd_.The.DocSearch.team.have.some.exciting.news.for.you.pdf)
It would be good to have something that demonstrates a popgen workflow. I converted one of @alimanfoo's [MalariaGEN analyses](https://github.com/alimanfoo/shiny-train) to use sgkit a while back (#232). The problem with converting...