Forum: Anyone using Ubuntu on Windows (WSL)?
0
gravatar for Batu
4 weeks ago by
Batu40
Batu40 wrote:

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...

wsl forum ubuntu • 205 views
ADD COMMENTlink modified 7 days ago • written 4 weeks ago by Batu40
1

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.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by h.mon18k

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.

ADD REPLYlink written 4 weeks ago by Batu40
1

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.

ADD REPLYlink written 4 weeks ago by genomax54k
1

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

ADD REPLYlink written 29 days ago by Batu40
1

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.

ADD REPLYlink written 4 weeks ago by jrj.healey5.9k
1

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.

ADD REPLYlink written 4 weeks ago by genomax54k

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

ADD REPLYlink written 4 weeks ago by Batu40
1

Did not realize there was no windows version available.

ADD REPLYlink written 4 weeks ago by genomax54k
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subread is available in conda/bioconda channels

ADD REPLYlink written 4 weeks ago by cpad01128.3k
4
gravatar for Batu
7 days ago by
Batu40
Batu40 wrote:

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!!

ADD COMMENTlink written 7 days ago by Batu40
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