if (!requireNamespace("easy16S", quietly = TRUE)) {
    # install.packages("remotes")
    remotes::install_gitlab(
        repo = "migale/easy16S@main",
        host = "forgemia.inra.fr"
    )
}

library(easy16S)
library(MicroBioMap)
library(phyloseq)
library(mia)

cpd <- getCompendium()
cpd_phyloseq <- convertToPhyloseq(x = cpd)
sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
rm(cpd)
gc()
sample_data(cpd_phyloseq)
cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
rm(cpd_phyloseq)
gc()
easy16S::run_app(physeq = cpd_phyloseq_europe)