gerlich_base.yml

name: ngs_base
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  # newest python
  - python = 3.9.9
  # user required tools:
  - cooler >= 0.8.8
  - numpy >= 1.18.5
  - sortedcontainers >= 2.2.2
  - matplotlib >= 3.2.2
  - multiprocess >= 0.70.10
  - pairtools >= 0.3.0
  - pandas >= 1.0.5
  - pybedtools >= 0.8.1
  - pybigwig >=0.3.17
  - pysam >= 0.16.0.1
  - scikit-learn >= 0.23.1 
  - scipy >= 1.5.0
  - seaborn >= 0.10.1
  - statsmodels >= 0.11.1
  # requirements for pairlib: 
  # - numpy
  - cython >= 0.29.20
  # requirements for bioframe:
  # - pandas 
  - six >=1.15.0
  - requests >= 2.24.0
  - pairix >= 0.3.7
  # requirements for cooltools:
  - h5py >= 2.10.0 
  - sparse
  - numba >= 0.48.0 
  - dask >= 2.19.0
  - click >= 7.1.2 
  - pytest >= 5.4.3
  # parquet support
  - pyensembl >= 1.8.7 
  - pyarrow >= 0.17.1
  - fastparquet >= 0.4.0 
  # jupyter support
  - jupyterlab >= 3.4.0
  # See: https://github.com/jupyterhub/jupyterhub/pull/4039
  - jupyterhub-singleuser=2.3.0
  - nodejs >= 13.12.0
  - plotly = 4.12.0
  - ipywidgets
  # loop caller
  - chromosight >= 1.1.4
  # image analysis
  - scikit-image
  - tifffile
  # plotting
  - graphviz
  - python-graphviz
  - umap-learn
  #more ngs tools
  - pip
  - pip:
      - biopython
      # for cbe batch environment 
      - batchspawner == 1.1.0
      - dask-labextension
      # read ROI files .zip or .roi generated with ImageJ
      - read-roi
      - shap
      - opencv-python-headless