Single-cell python bundle request

[laraPPr]

• link to support ticket: #2023091360000296 + #2023121860001271
• website: ...
• installation docs: ...
• toolchain: foss-2023a -> user prefers newer toolchain but not all packages are available in newer one
• easyblock to use: ...
• required dependencies:

1. Ready to use:

   • [x] SciPy-bundle-2023.07-gfbf-2023a
   • [x] matplotlib-3.7.2-gfbf-2023a
   • [x] Seaborn-0.13.2-gfbf-2023a

   • [x] PyTorch-2.1.2-foss-2023a / PyTorch-2.1.2-foss-2023a-CUDA-12.1.1

2. Need update:

   • [x] scanpy - only for 2022a (scanpy-1.9.1-foss-2022a.eb includes session_info which they also want)
   • [x] * scvi-tools-0.16.4-foss-2021a.eb / scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb (mudata, scvi-tools)
   • [x] * scArches-0.5.6-foss-2021a.eb / CUDA-11.3.1.eb (muon, sklearn, scArches)
   • [x] scib-metrics-0.3.3-foss-2021a.eb
   • [x] scVelo-0.2.3-foss-2021a.eb
   • [x] CellTypist-1.0.0-foss-2021b.eb
   • [x] loompy-3.0.7-foss-2022a.eb
   • [x] epiScanpy-0.4.0-foss-2022a.eb
   • [x] CellRank-1.4.0-foss-2021a.eb They want newer version at least v2
   • [x] scCODA-0.1.9-foss-2021a.eb
   • [x] rpy2-3.4.5-foss-2021b.eb
   • [x] infercnvpy-0.4.2-foss-2022a.eb
   • [x] pySCENIC-0.12.1-foss-2022a.eb

   • [x] Squidpy-1.2.2-foss-2021b.eb

3. Need create:

   • [x] Anndata2ri https://pypi.org/project/anndata2ri/
   • [x] Bbknn https://pypi.org/project/bbknn/
   • [x] Cassiopeia lineage https://pypi.org/project/cassiopeia-lineage/
   • [x] Sc_toolbox https://pypi.org/project/sc-toolbox/
   • [x] Altair https://pypi.org/project/altair/
   • [x] Pertpy https://pypi.org/project/pertpy/
   • [x] Tasccoda https://pypi.org/project/tascCODA/
   • [x] Liana-py https://pypi.org/project/liana/ !There is already an easyconfig for the Liana which is a R-package - not the same
   • [x] Harmonypy https://pypi.org/project/harmonypy/
   • [x] Scirpy https://pypi.org/project/scirpy/
   • [x] CellPhoneDB https://pypi.org/project/CellphoneDB/
   • [x] Decoupler https://pypi.org/project/decoupler/
   • [x] contrastiveVI https://github.com/suinleelab/contrastiveVI
   • should be part of scvi-tools now
   • https://github.com/suinleelab/contrastiveVI/tree/main?tab=readme-ov-file#user-guide
   • [x] Schist https://github.com/dawe/schist
   • effort: (TBD)
   • other install methods
   • conda: no
   • container image: no
   • pre-built binaries (RHEL8 Linux x86_64): no
   • easyconfig outside EasyBuild: yes / no

[pavelToman]

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20116

[laraPPr]

They have opened a bunch of new tickets for stuff that is in the list but not yet in the bundle. Maybe it can be used as a guide for which part to look at next:

ASAP

• [x] #2024051360000881 scvi-tools + mudata + scArches + scib-metrics

medium

• [x] #2024051360000916 Muon
• [x] #2024051360000925 harmonypy (listed as extension in Single-cell bundle)
• [x] #2024051360000934 CellPhoneDB (listed as extension in Single-cell bundle)
• [x] #2024051360000943 Decoupler-py (listed as extension in Single-cell bundle)
• [x] #2024051360000952 Liana (listed as extension in Single-cell bundle)
• [x] #2024051360000961 MuData (listed as extension in Single-cell bundle)
• [x] #2024051360000971 Scirpy (listed as extension in Single-cell bundle)
• [x] #2024051360001004 Pertpy
• [x] #2024051360001013 Schist

[pavelToman]

scvi-tools + scArches + scib-metrics + Pertpy + contrastiveVI are stoped and waiting for jax:

• https://github.com/easybuilders/easybuild-easyconfigs/pull/20119

Edit: jax without CUDA created from PR #20119