Function for creating symbolic links to view BAM files in a genome browser such as IGV.

symLink2bam(sysargs, command="ln -s", htmldir, ext = c(".bam", ".bai"), urlbase, urlfile)

Arguments

sysargs

Object of class SYSargs or SYSargs2 or named character vector with BAM files PATH and the elements names should be the sampleID.

command

Shell command, defaults to "ln -s"

htmldir

Path to HTML directory with http access.

ext

File name extensions to use for BAM and index files.

urlbase

The base URL structure to use in URL file.

urlfile

Name and path of URL file.

Value

symbolic links and url file

Author

Thomas Girke

Examples

## Construct SYSargs2 object from param and targets files 
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
args <- loadWorkflow(targets=targets, wf_file="hisat2/hisat2-mapping-se.cwl", 
                  input_file="hisat2/hisat2-mapping-se.yml", dir_path=dir_path)
args <- renderWF(args, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
args
#> Instance of 'SYSargs2':
#>    Slot names/accessors: 
#>       targets: 18 (M1A...V12B), targetsheader: 4 (lines)
#>       modules: 1
#>       wf: 0, clt: 1, yamlinput: 7 (inputs)
#>       input: 18, output: 18
#>       cmdlist: 18
#>    Sub Steps:
#>       1. hisat2-mapping-se (rendered: TRUE)
#> 
#> 

if (FALSE) {
## Run alignments
args <- runCommandline(args, dir = FALSE, make_bam = TRUE)

## Create sym links and URL file for IGV
symLink2bam(sysargs=args, command="ln -s", htmldir=c("~/.html/", "somedir/"), ext=c(".bam", ".bai"), urlbase="http://myserver.edu/~username/", urlfile="IGVurl.txt")
}