Running FastQC in R from a Windows Machine about fastqcr HOT 11 OPEN

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).

from fastqcr.

Hello,

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

Best

from fastqcr.

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!

from fastqcr.

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.

from fastqcr.

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

from fastqcr.

any updates on this?

from fastqcr.

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

from fastqcr.

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

from fastqcr.

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()

from fastqcr.

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

Thanks in advanced!

from fastqcr.

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!

from fastqcr.