symLink2bam: Symbolic links for IGV

In systemPipeR: systemPipeR: NGS workflow and report generation environment

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
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 SYSargs object from param and targets files 
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)

## Not run: 
## Construct SYSargs2 object from cwl and targets files
targets <- system.file("extdata", "targets.txt", package="systemPipeR") 
dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR") 
args <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl", input_file="hisat2-mapping-se.yml", dir_path=dir_path)  
args <- renderWF(args, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))

## 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)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.