R/bedr.setup.R

In uclahs-cds/public-R-bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
# (either version 1, or at your option, any later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text.
# OICR makes no representations whatsoever as to the SOFTWARE contained herein.  It is experimental in nature and is provided WITHOUT
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# By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or
# nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE.
# If publications result from research using this SOFTWARE, we ask that the Ontario Institute for Cancer Research be acknowledged and/or
# credit be given to OICR scientists, as scientifically appropriate.

bedr.setup <- function(datasets = "all", data.dir = paste0(Sys.getenv("HOME"),"/bedr/data")) {

	config.file <- paste0(Sys.getenv("HOME"),"/bedr/config.txt");
	if (!file.exists(data.dir)) dir.create(data.dir, recursive = TRUE);
	if (!file.exists(config.file)) file.create(config.file);

	config.bedr$data.dir <- data.dir;
	cat(as.yaml(config.bedr), file = config.file, append = TRUE);

	download.datasets(datasets, data.dir);
	
	return();
	}