Medaka

[laraPPr]

• link to support ticket: 2024070360000842
• website: https://github.com/nanoporetech/medaka
• installation docs: https://github.com/nanoporetech/medaka
• toolchain: foss/2023b
• toolchain: foss/2023a
• easyblock to use: PythonBundle
• required dependencies:
  • [ ]
• optional dependencies:
  • [ ] Flye
  • [ ] Dorado
• notes:
  • ...
• effort: (TBD)
• other install methods
  • conda: yes (link?) / no
  • container image: yes (link?) / no
  • pre-built binaries (RHEL8 Linux x86_64): yes (link?) / no
  • easyconfig outside EasyBuild: yes / no

[boegel]

duplicate of #352, see PR for CPU-only version:

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20865

GPU variant requires:

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20358

[pavelToman]

362, https://github.com/vscentrum/vsc-software-stack/issues/361 and https://github.com/vscentrum/vsc-software-stack/issues/360 need to be compatible because the user wants to use them together

[pavelToman]

After meeting 2/8/24 -> stick to foss/2023a not 2023b

[boegel]

PR for medaka 1.12.0 with CUDA was opened by @PetrKralCZ, and is merged:

• https://github.com/easybuilders/easybuild-easyconfigs/pull/21210

I've also opened PRs for the latest medaka 1.12.1, which were trivial updates:

• https://github.com/easybuilders/easybuild-easyconfigs/pull/21214
• https://github.com/easybuilders/easybuild-easyconfigs/pull/21215

Ready for cleanup & closing!