sctoolbox_env.yml

# This environment mainly holds dependencies that are needed to run the notebooks.
# Dependencies needed to run the sctoolbox should be put into the setup.py or pyproject.toml if possible.

name: sctoolbox
channels:
    - bioconda
    - conda-forge
dependencies:
# jupyter dependencies
  - notebook==6.5.2
  - ipykernel  # needed to register environment as jupyter kernel
# Dependencies used within the notebooks (but not the sctoolbox package)
  - pip>=24.2  # for installing additional packages
  - pip:
    - scanpro>=0.4.0  # scanpro < 0.3.1 needs statannotations which causes versioning issues
    # PyPI does not accept direct links so non PyPI packages are installed here
    - git+https://gitlab.gwdg.de/loosolab/software/annotate_by_marker_and_features.git
    - git+https://github.com/Novartis/scar.git
    - git+https://github.com/rwiegan/scvelo.git
# sctoolbox related dependency exemptions
# R dependencies (needed to enable data R->Python conversion)
  - r-base
  - r-seurat
  - bioconductor-singlecellexperiment
  - rpy2
# Other
  - samtools>=1.9  # fixes https://github.com/merenlab/anvio/issues/1479
  - rust  # fixes ERROR: Failed to build installable wheels for some pyproject.toml based projects (gseapy)
  - pybedtools  # this will install bedtools and ensure it is setup to work with pybedtools