Download data from ANEMONE DB

wget is used to download data files recursively from ANEMONE DB. Your user name and a temporary password generated in the website are required.

Usage

wget_recursive(
  rel_url = "dist/",
  opts = c("--reject=.fastq.xz,.png", "--no-verbose"),
  ...,
  user = getOption("ranemone.user"),
  password = getOption("ranemone.password")
)

Arguments

rel_url

A relative URL from the server root. If a directory is given, it should end with a slash / for --no-parent to work as expected.

opts

Additional options passed to wget. --recursive --level=0 --no-parent --continue are preset. --directory-prefix is set from directory_prefix(). --http-user and --http-password are set from user and password arguments, respectively. Currently -N/--timestamping does not work with the server: "Last-modified header missing – time-stamps turned off."

...

Additional arguments passed to base::system2().

user

Your ANEMONE DB user name. Setting it via options(ranemone.user = "_") will be easier for repeated use.

password

"Data Download Password" generated in the "Member Menu > Settings > Data Download" page, not your login password. Setting it via options(ranemone.password = "_") will be easier for repeated use.

Value

The return value of base::system2().

Details

The directory tree starting from db.anemone.bio/ will be created under directory_prefix() according to the default behavior of wget -r, which is assumed by other functions in this package.

See also

https://db.anemone.bio/how-to-download-data/, https://www.gnu.org/software/wget/manual/wget.html

Examples

if (FALSE) { # \dontrun{
options(ranemone.directory_prefix = "prefix/path/to/data")
options(ranemone.user = "your-username")
options(ranemone.password = "generated-password") # not yours

ranemone::wget_recursive("dist/MiFish/ANEMONE/2023KibanS/2023KibanSRUN01/")

fs::dir_ls(directory_prefix()) # "db.anemone.bio"
} # }