root is owner of files created by msconvert

[tczauderna]

Hi,

I have pulled the image
docker pull chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
and I basically run it like this
docker run -it --rm -e WINEDEBUG=-all -v /your/data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/file.raw

It works beautifully, however, all files created by msconvert are owned by root.
Is this intended behaviour?
Can this be changed via parameters?

I have tried adding a user
--user "$(id -u):$(id -g)"
running
docker run -it --rm --user "$(id -u):$(id -g)" -e WINEDEBUG=-all -v /your/data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert /data/file.raw
but this causes an error
$WINEPREFIX is not owned by you

I have also tried to run wine_anyuser which doesn't cause the error from above
docker run -it --rm --user "$(id -u):$(id -g)" -e WINEDEBUG=-all -v /your/data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine_anyuser msconvert /data/file.raw
but then all files are owned by root as well.

Thanks!

[chambm]

If switching user with --user then use mywine instead of wine_anyuser. That will copy the WINEPREFIX and the output should be owned by the user.

[tczauderna]

Thank you for looking into this!

I tried mywine but this causes a permission denied issue and some follow-up problems from the mywine script.

mkdir: cannot create directory '/mywineprefix': Permission denied
cp: target '/mywineprefix/' is not a directory
ln: failed to create symbolic link '/mywineprefix//dosdevices/c:': No such file or directory
ln: failed to create symbolic link '/mywineprefix//dosdevices/z:': No such file or directory
wine: chdir to /mywineprefix
 : No such file or directory

Then I changed mywine.sh line 4 from
MYWINEPREFIX=/mywineprefix/ to
MYWINEPREFIX=$(pwd)/mywineprefix/
which solved the permission denied issue but then msconvert didn't work.

[bobabooey]

Did you ever figure out how to solve this problem of root owning files created by msconvert?

[chambm]

Does this happen with mywine with the latest container version?

[bobabooey]

I'm using the latest container version. I'm getting the same error tczauderna reported:

$ docker run -it --rm --user "$(id -u):$(id -g)" -e WINEDEBUG=-all -v "$(pwd)":/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses mywine msconvert --help
mkdir: cannot create directory '/mywineprefix': Permission denied
cp: target '/mywineprefix/' is not a directory
ln: failed to create symbolic link '/mywineprefix//dosdevices/c:': No such file or directory
ln: failed to create symbolic link '/mywineprefix//dosdevices/z:': No such file or directory

Note the same command works if I remove --user "$(id -u):$(id -g)" however any files created are owned by root which I'm trying to solve. Thanks.

[ryanjob42]

I believe the issue is that the folder /mywineprefix doesn't exist. I am able to fix the issue by mounting a local directory to that location in the container by adding -v ./mywineprefix:/mywineprefix like so. Note: you may need to create the mywineprefix folder via mkdir mywineprefix first.

docker run -it --rm -v ./.mywineprefix:/mywineprefix -v /your/data:/data proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses mywine msconvert /data/file.raw -o /data

In case anyone is running in Singularity (like I am), you would add -B ./mywineprefix:/mywineprefix instead, like below. Again, you may need to create the mywineprefix folder first using mkdir mywineprefix.

singularity exec -B ./mywineprefix:/mywineprefix -B /your/data:/data docker://proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses mywine msconvert /data/file.raw -o /data