R/check.binary.R

In 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
# WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION
# OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT.
# 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.

check.binary <- function(x = 'bedtools', verbose = TRUE) {

	default.path <- '';
	git.url <- '';
	return.flag <- FALSE;

	if ('bedtools' == x) {
		git.url <- 'https://github.com/arq5x/bedtools2';
		}
	else if ('bedops' == x) {
		git.url <- 'https://github.com/bedops/bedops';
		}
	else if ('tabix' == x) {
		git.url <- 'https://github.com/samtools/tabix';
		}

	catv(paste0('  * Checking path for ', x, '... ') );

	# check if binary is in path
	if ('' == Sys.which(x)) {
		catv(paste0('FAIL\n') );
		path <- Sys.getenv('PATH');

		if ('' == git.url) {
			catv(paste0('    It can be downloaded from here: ', git.url, '\n'));
			}
		}
	else {
		catv(paste0('PASS\n    ', Sys.which(x), '\n') );
		return.flag <- TRUE;
		}

	return(return.flag);
	}