Nothing
getDefaultReferenceDir <- function() {
trace.enter("getDefaultReferenceDir");
on.exit({ trace.exit() })
optval = getPipelineOption('ArrayExpressHTS.reference');
for (path in optval) {
if (file.exists(path)) {
return(path);
}
}
return("");
}
getOptionPathComponent <- function(optname) {
optvalue = getPipelineOption(optname)
if( is.null(optvalue) || nchar(optvalue) == 0) {
return("");
} else {
return(paste(optvalue, ":", sep=""));
}
}
initEnvironmentVariables <- function() {
trace.enter("initEnvironmentVariables");
on.exit({ trace.exit() })
addPathToPATH("/ebi/microarray/home/biocep/local/lib64/R/lib");
addPathToPATH("/ebi/microarray/home/biocep/local/lib64/R/bin");
addPathToPATH("/ebi/microarray/home/biocep/local/bin");
addPathToPATH("/ebi/microarray/sw/bin");
addPathToPATH("/ebi/research/software/Linux_x86_64/opt/java/jdk1.6/bin");
addPathToPATH("/usr/local/bin");
addPathToPATH("/bin");
addPathToPATH("/usr/bin");
addPathToPATH("/usr/X11R6/bin");
addPathToPATH("/usr/lib64");
addPathToPATH("/lib64");
addPathToPATH(getPipelineOption("ArrayExpressHTS.cufflinks"));
addPathToPATH(getPipelineOption("ArrayExpressHTS.samtools"));
addPathToPATH(getPipelineOption("ArrayExpressHTS.bwa"));
addPathToPATH(getPipelineOption("ArrayExpressHTS.mmseq"));
addPathToPATH(getPipelineOption("ArrayExpressHTS.bam2hits"));
addPathToPATH(getPipelineOption("ArrayExpressHTS.bowtie"));
addPathToPATH(getPipelineOption("ArrayExpressHTS.tophat"));
addPathToPATH(getPipelineOption("ArrayExpressHTS.fasta_formatter"));
}
removePathFromPATH = function(pathtoremove) {
# get the array of existing records
pathArray = unlist(strsplit(Sys.getenv('PATH'), ":"));
# get all but the path
pathArray = pathArray[ is.na(match(pathArray, pathtoremove)) ];
# assemble back and set the PATH
Sys.setenv('PATH' = paste(pathArray, collapse=":"));
}
addPathToPATH = function(newpath) {
# get the array of existing records
pathArray = unlist(strsplit(Sys.getenv('PATH'), ":"));
# get all but the path
# make sure the path newpath is not duplicated
pathArray = pathArray[ is.na(match(pathArray, newpath)) ];
# assemble back, add the path at the
# beginning and set the PATH variable
#
Sys.setenv('PATH' = paste(newpath, paste(pathArray, collapse=":"), sep=":"));
}
replacePathInPATH = function(oldpath, newpath) {
# get the array of existing records
pathArray = unlist(strsplit(Sys.getenv('PATH'), ":"));
# get all but the oldpath
# remove duplicates of oldpath
pathArray = pathArray[ is.na(match(pathArray, oldpath)) ];
# get all but the newpath
# remove duplicates of newpath
pathArray = pathArray[ is.na(match(pathArray, newpath)) ];
# assemble back, add the path at the
# beginning and set the PATH variable
#
Sys.setenv('PATH' = paste(newpath, paste(pathArray, collapse=":"), sep=":"));
}
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