novoalign is not F/LOSS

[kelly-sovacool]

NCLscan depends on novoalign from novocraft. Novocraft's software are not Free/Libre Open Source; they require purchasing a license for v4 and for parallel processing with v3.

Biowulf has such a license, so we can use it with modules:

module load novocraft
novoalign -h

Novoalign V4.03.05 - Build May 11 2022 @ 10:26:56
# License file: /usr/local/apps/novocraft/novoalign.lic
# Licensed to NIH - Open Helix Expires on: 08/03/2025 (DD/MM/YYYY)

Usage:
    novoalign [options]

To use novocraft sofware in a container, we have to add a license to the container during the build process:

singularity shell docker://nciccbr/charlie_nclscan:v0.1.0 bash
Singularity> novoalign -v

Error - You need a valid current license to use this product.
You can purchase a license or request a trial license from http://www.novocraft.com/buy-now/
Novoalign V3 and earlier can be used by non-profit organisations without a license with some limitations on functionality.

We need to figure out whether we need a new license to create a docker container with novoalign or if we can use the NIH license, and whether that container must be private or if it can be public on dockerhub.

Alternatively, we don't need a license if we only use novoalign v3. But will rolling back to an older version change the results of the pipeline?