environment.yml

# @Author   : Yang Liu
# @FileName : environment.yml
# @Software : NANOME project
# @Organization : JAX Li Lab
# @Website  : https://github.com/LabShengLi/nanome
name: nanome
channels:
  - bioconda
  - conda-forge
dependencies:
  - python=3.6 # need 3.6 for some software, ont-guppy-client-lib need >=3.6 <=3.8
  - pip
  - nodejs
  - scipy
  - seaborn
  - numpy
  - pandas
  - tabix
  - pytabix
  - pysam
  - parallel
  - biopython>=1.79
  - jinja2>=3.0.2
  - joblib>=1.1.0
  - matplotlib>=3.3.4
  - minimap2>=2.23
  - pillow>=8.3.2
  - samtools>=1.12
  - statsmodels>=0.12.2
  - rocksdb>=6.13.3
  - python-rocksdb>=0.7.0
  - cython>=0.29.24
  - openpyxl>=2.4.0
  - nanocomp>=1.16.1
  - h5py # due to tombo/DeepMod issue (resquiggle is ok for higher version), must < 3.0, ref: https://github.com/nanoporetech/tombo/issues/325
  - scikit-learn # NANOME needs >=0.23.2, but METEORE needs older version <=0.23.2, it needs old package for RF model load, ref: https://github.com/comprna/METEORE/blob/master/combination_model_prediction.py#L44, https://stackoverflow.com/questions/65758102/no-module-name-sklearn-forest-ensemble
  - ont_vbz_hdf_plugin # used for multi-fast5 and gz format, ref: https://github.com/jts/nanopolish/issues/620
  - ont-fast5-api # =3.0 needed by fast5mod, will upgrade by pip install for Megalodon, but it's ok for running both >3.0
  - tensorflow>=1.8.0, <=1.13.1  # deepsignal needs: https://github.com/bioinfomaticsCSU/deepsignal#installation  tensorflow (1.8.0<=tensorflow<=1.13.1)
  - pybedtools>=0.8.2 # nanome needs upper version of pybedtools, deal with NAs
  - tqdm>=4.60 # need by Megalodon, ref: https://github.com/nanoporetech/megalodon/issues/105
  - ont-tombo>=1.5.1
  - nanopolish>=0.14.0
  - pip:
      - xgboost<=1.5.2  # nanome model load need <=1.5.x
      - ont-pyguppy-client-lib>=6.4.6
      - deepsignal>=0.2.0
      - fast5mod==1.0.5
      - nanome-jax>=2.0.10
      - megalodon