Use repo2docker container with singularoty

Binder
,
1

Hello,
We are trying to use a container made with repo2Docker on our HPC system, but we are using singularity with our /home mounted automatically. We can’t access /home/jovyan when we launch our container.

Is there procedure to use repo2Docker with singularity ?

Thank you,

2

repo2docker has a --user-id flag. If you set that to the owner of your mounted directory does it work?

3

This option changes the user name, but it is still not recognized by our file system and belongs to root.

github action :

    - name: update jupyter dependencies with repo2docker
      uses: jupyterhub/repo2docker-action@master
      with:
        DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
        DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }}
        NOTEBOOK_USER: roussman

singularity creation :

singularity shell --env JUPYTER_ENABLE_LAB=yes        docker://roussman/pytudes
Singularity> ls -ls /home
total 1
0 drwxr-xr-x. 3 roussman ipadefaultgp 60 Mar 14 10:16 qt
1 drwxr-x---. 2 root     root         66 Mar 14 09:51 roussman
4

The username argument is separate from the user ID. You didn’t mention you were using the GitHub action- it doesn’t support the user-id argument, instead you could run repo2docker directly in your GitHub workflow.

5

I’ve tried setting the user_id as my own, but I still have the same problem. Another problem is that this container is to be used by several users, so I can’t set it for my account alone. I managed to access the repository inside the container by adding a chmod in the container creation. Can I add this option and make a merge request in the repo2docker project?

6

I’m surprised setting the user-id didn’t work. Can you share the full repo2docker command line and an example repository that you’re having problems with? Which version of repo2docker are you using?

1 Like
7

I have a fork of the main branch. I didn’t use the command, since I was already testing some modifications, I hard-coded my user_id app.py (l777).

8

I solved my issue by adding this chmod in the appendix option. Thank you for your help !

1 Like