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/conda-gpu_env.yml
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| a | b/conda-gpu_env.yml | ||
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| 1 | name: bpnet-gpu |
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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=3.6.13 |
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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>=0.14.0 |
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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>=2.7.0 |
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| 20 | - numpy |
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| 21 | |||
| 22 | - pandas>=0.23.0 |
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| 23 | - fastparquet |
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| 24 | - python-snappy |
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| 25 | |||
| 26 | - nb_conda=2.2.1 |
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| 27 | - pip |
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| 28 | - pip: |
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| 29 | - git+https://github.com/kundajelab/DeepExplain.git |
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| 30 | |||
| 31 | #Synchronized packages for Jupyter Notebooks |
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| 32 | - ipykernel==5.3.0 |
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| 33 | - ipython==7.15.0 |
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| 34 | - ipywidgets==7.5.1 |
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| 35 | - jupyter_client==6.1.3 |
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| 36 | - jupyter_core==4.6.3 |
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| 37 | - markdown==3.2.2 |
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| 38 | - nbconvert==5.6.1 |
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| 39 | - nbformat==5.0.6 |
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| 40 | - notebook==6.0.3 |
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| 41 | - papermill==2.1.1 |
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| 42 | - nbclient==0.4.0 |
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| 43 | |||
| 44 | # ML & numerics |
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| 45 | - tensorflow-gpu==1.7 #for gpu |
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| 46 | |||
| 47 | # bpnet package |
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| 48 | - .[dev,extras] # install the local basepair package. All the other required pip packages are specified in the setup.py |