#!/usr/bin/env Rscript
## code to mirror all raw datasets (which can be downloaded by users) of UCSC Xena
# Update to the recent UCSCXenaTools
# BiocManager::install("UCSCXenaTools")
suppressMessages(library(UCSCXenaTools))
library(furrr)
args <- commandArgs(trailingOnly = TRUE)
if (length(args) != 2) {
message("Error: two arguments are required!")
message()
message("Usage: ./mirror.R <destdir> <thread>")
message("Set thread to 0 to run sequentially.")
quit("no", status = 1)
}
destdir <- path.expand(args[1])
threads <- as.integer(args[2])
sink(file = file.path(destdir, "mirror.txt"))
on.exit(sink(NULL))
message("destdir: ", destdir)
message("threads: ", threads)
if (!dir.exists(destdir)) dir.create(destdir, recursive = TRUE)
if (threads != 0) {
future::plan(multisession, workers = threads)
call_fun <- furrr::future_map
} else {
call_fun <- purrr::map
}
download_dataset <- function(x, destdir) {
x %>%
XenaGenerate() %>%
XenaQuery() %>%
XenaDownload(
destdir = destdir,
download_probeMap = TRUE,
trans_slash = FALSE,
force = TRUE,
method = "curl", extra = "-C -") # 断点续传
}
access_datasets <- XenaData # XenaDataUpdate(saveTolocal = FALSE)
hubs <- unique(access_datasets$XenaHostNames)
dataset_list <- call_fun(hubs, function(h) {
sink(file = file.path(destdir, "mirror.txt"), append = TRUE)
x <- subset(access_datasets, XenaHostNames == h)
message("Mirroring hub: ", h)
message("================================")
download_dataset(x, file.path(destdir, h))
})
mapping_df <- Reduce(rbind, dataset_list)
message("================================")
message("The mirror work has done, please check the mirror.txt.")
write.csv(mapping_df,
file = file.path(destdir, "mapping_dataframe.csv"),
row.names = FALSE, quote = FALSE)
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