4. FAQs

4.1. A Fatal error: cannot open file occurred but the file is visible

This is most likely caused by the file residing on an NFS (network file system) mount that is not visible inside the container.

Fix it by setting the DAMONA_SINGULARITY_OPTIONS environment variable to bind the NFS mount into the container:

In a bash or zsh shell:

export DAMONA_SINGULARITY_OPTIONS="-B /mnt/my_space:/mnt/my_space"

In a fish shell:

set DAMONA_SINGULARITY_OPTIONS "-B /mnt/my_space:/mnt/my_space"

See the DAMONA_SINGULARITY_OPTIONS section of the user guide for more details and additional examples.

4.2. Why Damona and not conda/mamba?

Damona is not a replacement for conda/bioconda – it is a complementary tool with a different focus:

  • Reproducibility – Singularity images are immutable; running the same container on two different machines always produces the same result.

  • Isolation – Containers do not share libraries with the host system, so there are no dependency conflicts between tools.

  • HPC-friendly – Singularity/Apptainer does not require root privileges and is widely available on computing clusters where Docker is not permitted.

  • Easy sharing – A bundle file created with damona export can be given to a colleague who can recreate the exact same environment with damona env --from-bundle.

In practice many bioinformatics teams use both: conda for exploratory work and Damona for the stable, shared analysis pipelines that need to be reproducible over time.