Add/update software

[espenhgn]

Misc. maintenance items.

Add missing R libraries to r.sif:

• posit/CRAN:
  • R.matlab
  • rmatio
  • matlab
  • matlab2r
  • raveio
  • rhdf5
  • foreign
• posit/bioconductor:
• GitHub:
  • https://github.com/JianYang-Lab/gsmr2
• Source:
• Misc:

Add missing Python packages to python3.sif:

• Update base Python version to 3.12 or 3.13 from 3.10. Important packages like Numpy-2.3.0 have now dropped support for 3.10
  • Fixed via Python3.sif: fix broken ipython magic #321
• Build from Miniforge3 image as Mambaforge has been deprecated
  • Fixed via Python3.sif: fix broken ipython magic #321
• conda-forge:
  • pyreadr
  • pandas' optional packages
  • tabulate
• PyPI.org:
• GitHub:
• binaries:

Add missing binary tools to gwas.sif:

• https://github.com/freeseek/score - needs bumping bcftools >=v1.20
• https://github.com/wuyangf7/OPERA
• SMR

System deps: