symLink2bam | R Documentation |
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)
sysargs |
Object of class |
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. |
symbolic links and url file
Thomas Girke
## 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)
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