Sync‐meeting‐EMBL‐20240522

Sync with EMBL on EasyBuilding RFDiffusion, AlphaPulldown, RoseTTAFold-All-Atom (20240522)

AlphaFold (3.x)

• source release is expected to happen due to pressure of open source community
  • or someone else will re-implement it
• may be an interesting use case to install into EESSI
• Thomas included his PR to split up pipeline into multiple parts to parallellize it

AlphaPulldown

• cctbx is a PITA
  • AlphaPullDown (Jan Kosinski's group) is actively looking replacing cctbx with BioPython
    • see https://github.com/KosinskiLab/AlphaPulldown/issues/343
  • could still be interesting for PHENIX
  • EMBL has direct line of contact with them
  • Thomas @ EMBL is currently uses conda-approach for this
    • please share
  • separate easyconfig for AlphaLink2 (dep of AlphaPulldown 2.0)

RFDiffusion

• RFDiffusion starts downloading data on first use
• Thomas' PR: https://github.com/easybuilders/easybuild-easyconfigs/pull/18359
  • required Sam's PR: https://github.com/easybuilders/easybuild-easyconfigs/pull/20019

RoseTTAFold-All-Atom

• WIP @ UGent, see https://github.com/vscentrum/vsc-software-stack/issues/327

RoseTTAFold2NA

• see Jörg's PR: https://github.com/easybuilders/easybuild-easyconfigs/pull/20099

SE3-Transformer

• common dep of he above
• instal as separate module?

RELION

• cryo course at EMBL in OCt'24 with RELION developers
• cfr. open PR: https://github.com/easybuilders/easybuild-easyconfigs/pull/19678
• TOMO(graphy) pipeline is missing in Jasper's PR (new feature in RELION 5)
• some things like ctffind are not optional for RELION

EESSI

• also ship datasets through CernVM-FS? (via dedicated data.eessi.io repository)
  • would be interesting to get Varnish working instead of Squid for proxies

EasyBuild Slack

• new dedicated channels created: cryo-em + structure_prediction