symLink2bam: Symbolic links for IGV

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

Symbolic links for IGV

Description

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

Usage

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(s)

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

## Not run: 
## 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")

## End(Not run)

tgirke/systemPipeR documentation built on June 13, 2025, 1:38 p.m.