symLink2bam {systemPipeR} | R Documentation

## 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 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)

[Package systemPipeR version 2.0.8 Index]