Running FastQC in R from a Windows Machine

[qpmnguyen]

Hi!

I installed the package in R and tried to run it (using the fastqc() function) but there was a check on whether or not my system was unix based and gave an error.

I was wondering if either fastqcr does not support running from a windows machine or I just accidentally installed a version that is only for unix machines (I did not use the function fastqc_install)

Thanks!

[tbersez]

Hello,

I have the same problem, did you solved it? (I did not used fastqc_install either)

Best

[qpmnguyen]

I have not been able to solve this issue either. I think it's because the R package is a wrapper for the unix/linux versions of fastqc and not the windows version so the R-package doesn't work with windows computers. I just use fastqc from the command line instead of the R package.

Hope this helps!

[drescs]

I'm also having this problem, would love if there were a fix! I may be able to just do my work on another PC but obviously that's a bit inconvenient.

[VicSales]

The error is still happening: Error in .check_if_unix() : Unix system (MAC OSX or Linux) required.

[arodzh-sudo]

any updates on this?

[rdinnager]

I don't know why Windows isn't supported in this package. Would you accept a pull request to add Windows support? It doesn't appear to be difficult but perhaps there is some reason I am unaware of?

At the very least I suggest removing the .check_if_unix() to allow people to at least use Windows Subsystem for Linux. As a hack to get it running I installed FastQC on my Windows Subsystem for Linux and then got fastqcr::fastqc() running by writing over .check_if_linux() inside fastqcr with this code:

.check_if_unix <<- function() {
  return(NULL)
}
assignInNamespace(".check_if_unix", .check_if_unix, ns = "fastqcr")

Then I can run:

fastqcr::fastqc("fastq_path", fastqc.path = "wsl.exe /path_to_wsl_fastqc_install/fastqc")

And it works fine! wsl.exe /path_to_wsl_fastqc_install/fastqc runs FastQC inside Windows Subsystem for Linux (wsl.exe).

[kassambara]

@rdinnager a pull request is very welcome! thank you in advance for your contribution

[pfrombris]

Any progress on this? I'd also like to be able to run this package on Windows.

[rbabaei82]

I could not find any solution, but there are alternatives to FastQC in r for Windows. you can try one of these. Doing the same job with some differences in the plot. Rqc::rqcReport() QuasR::qQCReport() systemPipeR::seeFastq() ShortRead::report()

[ulazcanoCICbioGUNE]

Hello I find that the problem remains, is there any progress to adress this issue?

Thanks in advanced!

[Sheficm]

The error is still happening: Error in .check_if_unix() : Unix system (MAC OSX or Linux) required.

Any update on this? could you resolve this?

Thanks in advance!