Installation script

[MolbioUnige]

Hi,
I wasn't able to install nextPYP using a service account as PYP_USER on Ubuntu. I had to use my admin account. It seems that it is not possible to do sudo -u (used in the script) with a non-sudoer account. I tried on different machines, I always get a permission denied response. I couldn't find any answer to this problem. Would you have any suggestions?
Thanks

[MolbioUnige]

I have another question regarding the installation script. What is the use of creating the /home/$username/ directory? Is it for slurm? Can I do without it if it's installed on a single server?

[cuchaz]

The installation script is designed to be run under sudo. So you'd run the installer like: sudo A=a B=b ./install. That should give the installation script enough permissions to continue.

The home directory for the service account is required by apptainer. Without it, the containers fail to launch.

[MolbioUnige]

Thank you for your answer.
There is a problem with Ubuntu I think. I could not run the installation script unless the folder where nextPYP were to be installed was w+x by PYP_USER or PYP_GROUP. It could then proceed but then failed at creating the home directory:

sudo PYP_USER=nextpyp PYP_DOMAIN=my.domain ./install
nextpyp:x:150:
Installing nextPYP 0.5.1 for user nextpyp on domain my.domain ...
Downloading installation files ...
2023-11-10 14:59:58 URL:https://nextpyp.app/files/pyp/0.5.1/nextPYP.sif [438743040/438743040] -> "nextPYP.sif" [1]
2023-11-10 15:00:00 URL:https://nextpyp.app/files/pyp/0.5.1/reverse-proxy.sif [16678912/16678912] -> "reverse-proxy.sif" [1]
2023-11-10 15:03:50 URL:https://nextpyp.app/files/pyp/0.5.1/pyp.sif [4816891904/4816891904] -> "pyp.sif" [1]
2023-11-10 15:03:51 URL:https://nextpyp.app/files/pyp/0.5.1/hostprocessor [1580/1580] -> "hostprocessor" [1]
2023-11-10 15:03:51 URL:https://nextpyp.app/files/pyp/0.5.1/start [4901/4901] -> "start" [1]
2023-11-10 15:03:52 URL:https://nextpyp.app/files/pyp/0.5.1/stop [45/45] -> "stop" [1]
2023-11-10 15:03:52 URL:https://nextpyp.app/files/pyp/0.5.1/startrprox [272/272] -> "startrprox" [1]
2023-11-10 15:03:53 URL:https://nextpyp.app/files/pyp/0.5.1/stoprprox [51/51] -> "stoprprox" [1]
2023-11-10 15:03:53 URL:https://nextpyp.app/files/pyp/0.5.1/install-systemd [2012/2012] -> "install-systemd" [1]
2023-11-10 15:03:54 URL:https://nextpyp.app/files/pyp/0.5.1/uninstall-systemd [567/567] -> "uninstall-systemd" [1]
2023-11-10 15:03:54 URL:https://nextpyp.app/files/pyp/0.5.1/uninstall [431/431] -> "uninstall" [1]
2023-11-10 15:03:55 URL:https://nextpyp.app/files/pyp/0.5.1/workflows/spr_tutorial.toml [3881/3881] -> "/opt/nextPYP/workflows/spr_tutorial.toml" [1]
2023-11-10 15:03:55 URL:https://nextpyp.app/files/pyp/0.5.1/workflows/tomo_tutorial.toml [7580/7580] -> "/opt/nextPYP/workflows/tomo_tutorial.toml" [1]
2023-11-10 15:03:56 URL:https://nextpyp.app/files/pyp/0.5.1/workflows/class_tutorial.toml [7220/7220] -> "/opt/nextPYP/workflows/class_tutorial.toml" [1]
Created local directory: /opt/nextPYP/local
Created shared directory: /opt/nextPYP/shared
mkdir: cannot create directory ‘/home/nextpyp’: Permission denied

I modified the script so that it creates the directory as the admin account and then change it's ownership to PYP_USER:PYP_GROUP

  105 # create configuration file
  106 mkdir -p "/home/$username/.config"
  107 chown -R "$username:$usergroup" "/home/$username"

Now it succeeded.

[cuchaz]

Ah, yes. The current directory should be writable by the chosen user. And we should definitely change the installer to set the correct permissions on the home folder for the service account. It's weird that we've never run into these problems before in our testing, but thanks for the info! We're working on updating the install process to make it easier and we'll make sure to include these changes.

[abartesaghi]

These issues have been addressed in v0.5.2.