Forum:Anyone using Ubuntu on Windows (WSL)?

Question

[Batu]

I've been using Ubuntu on WSL, and I didn't have any problem since I have an error in featureCounts (Segmentation failed (core dumped) error in featureCounts ). And I started to believe that something is broken in WSL and it causes an error on our computers when running featureCounts. After my friend also got the same error on the computer with 64 GB of RAM, I started to think that obviously that error I got in feeatureCounts is not about the amount of RAM.

Are you using Ubuntu on Windows? Have you experienced any problem in WSL? Thanks.

[h.mon]

I moved your post from "Question" to "Forum", as it seems more fit.

I never used Linux on Windows (or whatever name it is called nowadays - Windows Subsystem for Linux?), but read here and elsewhere compatibility is very good, towards 100% - but not 100%. One thing to be aware is t never write on the Linux area from Windows tools.

If you had problems on more than one computer with featureCounts, it may well be it is not compatible. It is be worth opening a bug report, in case WSL provides means to do so.

[Batu]

I should really report that to WSL developers. I was thinking that I can work all tools natively on WSL. When I see that problem, it disappointed me, and made me see that I shouldn't fully trust on WSL, sadly.

[GenoMax]

WSL is not a mainstream feature in Windows (which is why you have to go out of the way to install it). I don't think it is meant for production use.

[Batu]

I have reported this issue to Microsoft, FYI https://github.com/Microsoft/WSL/issues/3391

[Joe]

It's definitely not 100% identical, but I have to say I've not encountered any problems so far (but I don't use it for work/bioinformatics).

You might want to try installing something like Cygwin to see if you can replicate the issue.

[GenoMax]

featureCounts is also available as a part of a R package. You could try to see if it works natively on R in windows.

You may also want to check into this.

[Batu]

I checked and I found Rsubread package cannot be installed on Windows.

[GenoMax]

Did not realize there was no windows version available.

[cpad0112]

subread is available in conda/bioconda channels

Answer 1

[Batu]

Workaround for this problem is to recompile subread package with the recent glibc (https://github.com/Microsoft/WSL/issues/3391). To do that, update glibc to the newest version (2.23), and then compile the source of the package, and introduce its "bin" directory to path. Problem solved!!