Running notebook on singularity

[jooh]

Has anyone managed to get the tutorial to run under singularity? I just did a pull and conversion with

singularity pull docker://miykael/nipype_tutorial:latest

There seems to be something funny about the path inside the image - jupyter isn't on it.

singularity exec -C nipype_tutorial-latest.simg jupyter notebook
/.singularity.d/actions/exec: 9: exec: jupyter: not found
singularity exec -C nipype_tutorial-latest.simg bash
jc01@login27:~$ which jupyter
jc01@login27:~$ ls
jc01@login27:~$ ls /
bin   data  environment  home  lib64  mnt          opt     proc  run   singularity  sys  usr
boot  dev   etc          lib   media  neurodocker  output  root  sbin  srv          tmp  var

[miykael]

Hi @jooh - I haven't run the tutorial with singularity yet, so I'm not sure how much I can be of help. But I might be able to give you some pointers.

In the docker file, jupyter is located at /opt/miniconda-latest/envs/neuro/bin/jupyter. Are the MATLAB_MCR and SPM12 folders under /opt. What about the nipype_tutorial content? Is it under /home/neuro/nipype_tutorial?

Looking at neurodockers example on how to create the Dockerfile or the Singularity file I saw that singularity omitts the --cmd jupyter-notebook at the end. (see for docker and singularity here).

Also, from the instructions on neurodocker that you can:

# Start jupyter-notebook
$ singularity run nipype_tutorial.sqsh jupyter-notebook
# Start interactive bash shell
$ singularity run nipype_tutorial.sqsh

Alternatively, you could also create the Singuliarty image yourself with the example under neurodocker.

Does any of this help somehow?