symLink2bam.Rd
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)
Object of class SYSargs
or SYSargs2
or named character vector
with BAM files PATH and the elements names should be the sampleID.
Shell command, defaults to "ln -s"
Path to HTML directory with http access.
File name extensions to use for BAM and index files.
The base URL structure to use in URL file.
Name and path of URL file.
symbolic links and url file
## 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")
}