gdc_cache: Work with gdc cache directory

In Bioconductor/GenomicDataCommons: NIH / NCI Genomic Data Commons Access

Work with gdc cache directory

Description

The GenomicDataCommons package will cache downloaded files to minimize network and allow for offline work. These functions are used to create a cache directory if one does not exist, set a global option, and query that option. The cache directory will default to the user "cache" directory according to specifications in app_dir. However, the user may want to set this to another direcotory with more or higher performance storage.

Usage

gdc_cache()

gdc_set_cache(
  directory = rappdirs::app_dir(appname = "GenomicDataCommons")$cache(),
  verbose = TRUE,
  create_without_asking = !interactive()
)

Arguments

directory	character(1) directory path, will be created recursively if not present.
verbose	logical(1) whether or not to message the location of the cache directory after creation.
create_without_asking	logical(1) specifying whether to allow the function to create the cache directory without asking the user first. In an interactive session, if the cache directory does not exist, the user will be prompted before creation.

Details

The cache structure is currently just a directory with each file being represented by a path constructed as: CACHEDIR/UUID/FILENAME. The cached files can be manipulated using standard file system commands (removing, finding, etc.). In this sense, the cache sytem is minimalist in design.

Value

character(1) directory path that serves as the base directory for GenomicDataCommons downloads.

the created directory (invisibly)

Functions

• gdc_set_cache(): (Re)set the GenomicDataCommons cache directory

Examples

gdc_cache()
## Not run: 
gdc_set_cache(getwd())

## End(Not run)

Bioconductor/GenomicDataCommons documentation built on Oct. 31, 2024, 7 a.m.