requirements.yaml

name: gimme
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - biofluff >=3.0.4              # necessary for coverage_table()
  - configparser
  - diskcache
  - feather-format
  - genomepy >=0.13.0
  - ipywidgets                    # optional: progress bar in Jupyter notebook
  - iteround
  - jinja2
  - logomaker
  - loguru
  - matplotlib-base >=3.3         # https://matplotlib.org/stable/devel/min_dep_policy.html#list-of-dependency-versions
  - numpy >=1.18                  # https://numpy.org/neps/nep-0029-deprecation_policy.html#support-table
  - pandas >=1.3.0                # version necessary for ExtraStyler.render()
  - pybedtools >=0.9.0
  - pysam >=0.16
  - python >=3.6
  - python-xxhash
  - qnorm  >=0.8.1
  - scikit-learn >=0.23.2         # https://scikit-learn.org/stable/install.html#installing-the-latest-release
  - scipy >=1.5                   # https://docs.scipy.org/doc/scipy/dev/toolchain.html#numpy
  - seaborn >=0.10.1
  - statsmodels
  - tqdm >=4.46.1
  - xdg
  #  - xgboost >=1.0.2            # optional: xgboost regression predictor for MOAP. 1 GB

  # motif discovery tools
  - gcc                           # optional: necessary to install motif discovery tools
  # AMD                           # installed from source
  # BioProspector                 # installed from source
  # ChIPMunk                      # installed from source
  - dinamo >=1.0                  # optional
  # DREME                         # not available
  - gadem >=1.3.1                 # optional
  # HMS                           # installed from source
  - homer >=4.11                  # optional
  # Improbizer                    # installed from source
  # MDmodule                      # installed from source
  - meme >=5.4.1                  # optional
  # MEMEW                         # installed from source
  # MotifSampler                  # installed from source
  # Posmo                         # installed from source
  - prosampler >=1.0              # optional
  # RPMCMC                        # not available
  - trawler >=2.0                 # optional. 200 MB
  - weeder >=2.0                  # optional. 100 MB
  - xxmotif >=1.6                 # optional
  #  - yamda >=0.1.00e9c9d        # optional. 3 GB

  # development packages
  - black=22.3.0                  # same as in .pre-commit-config.yaml
  - flake8=4.0.1                  # same as in .pre-commit-config.yaml
  - flake8-bugbear=22.4.25        # same as in .pre-commit-config.yaml
  - isort=5.10.1                  # same as in .pre-commit-config.yaml
  - pre-commit
  - pytest
  - pytest-cov