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/conda-env.yml
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| a | b/conda-env.yml | ||
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| 1 | name: bpnet |
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| 2 | channels: |
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| 3 | - bioconda |
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| 4 | - pytorch |
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| 5 | - conda-forge |
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| 6 | - defaults |
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| 7 | dependencies: |
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| 8 | - python=3.6 |
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| 9 | |||
| 10 | # genomics |
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| 11 | - pybedtools==0.7.10 |
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| 12 | - bedtools==2.27.1 |
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| 13 | - pybigwig>=0.3.10 |
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| 14 | - pysam==0.15.3 |
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| 15 | - genomelake==0.1.4 |
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| 16 | |||
| 17 | - pytorch # optional for data-loading |
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| 18 | - cython |
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| 19 | - h5py==2.9.0 |
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| 20 | - numpy==1.18.5 |
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| 21 | - tqdm==4.46.1 |
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| 22 | - scipy==1.4.1 |
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| 23 | - statsmodels==0.11.1 |
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| 24 | - scikit-learn==0.21.3 |
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| 25 | |||
| 26 | - pandas==1.0.3 |
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| 27 | - fastparquet==0.4.0 |
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| 28 | - python-snappy |
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| 29 | |||
| 30 | - nb_conda |
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| 31 | - pip |
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| 32 | - pip: |
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| 33 | - git+https://github.com/kundajelab/DeepExplain.git |
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| 34 | |||
| 35 | # ML & numerics |
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| 36 | - tensorflow>=1.7,<=1.14 # tensorflow-gpu==1.7 for gpu |
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| 37 | |||
| 38 | - kipoiseq==0.3.4 |
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| 39 | - kipoi==0.6.25 |
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| 40 | - joblib==0.15.1 |
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| 41 | |||
| 42 | # bpnet package |
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| 43 | - .[dev,extras] # install the local basepair package. All the other required pip packages are specified in the setup.py |