symLink2bam: Symbolic links for IGV

Description Usage Arguments Value Author(s) Examples

View source: R/utilities.R

Description

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

Usage

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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

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## 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", 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_"))

## 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 Sept. 18, 2021, 12:03 p.m.