Image build failing.

[andzajan]

Hi, I was getting error "source" not found while trying to build an image using Singularity 3.8.1.

Problem was solved by changing line 14 (https://github.com/hyoo/alphafold_singularity/blob/main/alphafold.def#L14) to:

. /opt/miniconda3/etc/profile.d/conda.sh

[hyoo]

This is related to the shell. Are you using bash?
https://askubuntu.com/questions/25488/what-is-the-difference-between-source-and

[andzajan]

Yes, building from Ubuntu 20.04 and I guess that builder is executing "source" on the host OS, so I don't know why during my build it's not using bash. I am not very experienced with Singularity.

[aeszter]

I've encountered the same error when building on openSUSE, where /bin/sh is symlinked to bash. So maybe source was called inside the container after all?

[fredricj]

The default shell in singularity is /bin/sh, i.e. bash in posix mode. Changing %post to %post -c /bin/bash switches to using bash instead which would fix this error and also prevent other errors with non-posix syntax in other shell scripts used by conda