Export folder permissions root root?

[jjkoehorst]

I have extended the docker image to load in some internal applications.

These applications when executed can create a dependency folder and download some related applications from our internal resources.

However I have a feeling that something goes off with the permissions.

I have created and extended the docker tools with an additional folder. In this folder is a list of jar files and corresponding galaxy xml files all as user galaxy group galaxy.

However when using -v to mount /export to a local empty folder all the files that are copied become root? This is happening on an ubuntu system but on an Mac system the files become according to my user account.

I am not sure if this is a docker issue and not necessary a galaxy issue?

I managed to solve it temporarily by starting Portainer and run a bash environment and go to /export and chown -R galaxy everything as shown in #163 but I assume this is not the correct way of doing this?

[bgruening]

Hi @jjkoehorst. This is a Docker "problem" as it seems. On your host system files are then stored under root. However, inside the container is should still be accessible, right? Have a look at the --user option of the docker run command. Maybe this can help.

[jjkoehorst]

The problem is that docker then uses the /export/ location which then needs root privileges. The galaxy user which I assume starts galaxy does not have these privileges and therefor cannot make files and folders in the tools directory. I wil dive into it further but the “fix” is to use Portrainer to set the folder rights to galaxy:galaxy

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On 5 Feb 2018, at 14:28, Björn Grüning ***@***.***> wrote: Hi @jjkoehorst <https://github.com/jjkoehorst>. This is a Docker "problem" as it seems. On your host system files are then stored under root. However, inside the container is should still be accessible, right? Have a look at the --user option of the docker run command. Maybe this can help. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#415 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEQ7k92r0LkzBuAfCokoVaTfHkZsbTOdks5tRwIZgaJpZM4R5J5E>.