Single-cell-python-bundle

[boegel]

• link to support ticket: #2025121160000833 (indirect request)
• website: (bundle)
• installation docs: (bundle)
• toolchain: foss/2024a
• easyblock to use: (see existing easyconfig)
• required dependencies:
  • (see existing easyconfig)
• notes:
  • should include:
    • Palantir (new), see: Palantir #606
    • updated scvi-tools, see: scvi-tools #625
• 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
• PRs:
  • {bio}[foss/2024a] Palantir v1.4.1 easybuilders/easybuild-easyconfigs#25669
  • {bio,tools}[foss/2024a] bin2cell v0.3.4, stardist v0.9.1, CSBDeep v0.8.2, cramjam v2.11.0, fastparquet v2026.3.0 easybuilders/easybuild-easyconfigs#25667
  • {bio}[foss/2024a] Cassiopeia v2.1.0-2025-10-9, Squidpy v1.6.6, CVXPY v1.5.1, Clarabel.rs v0.11.1 easybuilders/easybuild-easyconfigs#25596
  • {bio}[foss/2024a] CellBender v0.3.2, jupyter-contrib-nbextensions v0.7.0 w/ CUDA 12.6.0 easybuilders/easybuild-easyconfigs#25636
  • {bio}[foss/2024a] scib-metrics v0.5.9 w/ CUDA 12.6.0 easybuilders/easybuild-easyconfigs#25601
  • {bio}[foss/2024a] scArches v0.6.1 w/ CUDA 12.6.0 easybuilders/easybuild-easyconfigs#25598
  • {bio}[foss/2024a] scCODA v0.1.9, scikit-bio v0.6.3 easybuilders/easybuild-easyconfigs#25476
  • {bio}[foss/2024a] CellRank v2.0.7 easybuilders/easybuild-easyconfigs#25579
  • {lib}[foss/2024a] scib v1.1.7, CellTypist v1.7.1, libleidenalg v0.11.1, ... easybuilders/easybuild-easyconfigs#25479
  • {bio}[foss/2024a] scVelo v0.3.4 easybuilders/easybuild-easyconfigs#25478
  • {bio}[foss/2024a] epiScanpy v0.4.0 easybuilders/easybuild-easyconfigs#25477
  • {bio}[foss/2024a] pySCENIC v0.12.1-20250109 easybuilders/easybuild-easyconfigs#25474
  • {bio}[foss/2024a] infercnvpy v0.6.1 easybuilders/easybuild-easyconfigs#25475