Updates to MST - Githubissues

bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

https://www.bacpop.org/poppunk

Apache License 2.0

89 stars 18 forks source link

Closed nickjcroucher closed 3 years ago

nickjcroucher commented 3 years ago

Minor updates:

MST plots now work with lineages
--previous-clustering now requires a specific file in both visualise and plot_mst modes
test updated accordingly

Not sure about:

as sparse_mst.py still requires --distances, do we still require calculation of all-v-all, or are we just using the "metadata" without calculating the values?

nickjcroucher commented 3 years ago

(I don't know why endswith() works, where the regex was failing - could not figure this out).

johnlees commented 3 years ago

Can we also pin the version of graph-tool, had a few reports of that going wrong. i.e. modify environment.yml to:

graph-tool >=2.35

nickjcroucher commented 3 years ago

Added cugraph and cudf to environment.yml in 3e5160e.