Installation - deephelicon

Overview¶

We tested DeepHelicon on a Linux operating system, as several input feature generation tools are Linux-dependent. However, if you already have the required feature files (as shown in example_data), the program can be run on other platforms such as Windows and macOS. Before using the software, please ensure that Python (version >=3.11) is installed. We highly recommend using Anaconda, an integrated Python development environment, which simplifies package management and environment setup.

Installing¶

GitHub¶

Then, we can follow the step-by-step precedures for installation.

Step 1: Get the most recent version of DeepHelicon from GitHub (clone it at your preferred location), PyPI, or Conda.

git clone https://github.com/2003100127/deephelicon.git

Step 2: Create a conda environment in your local machine.

conda create --name deephelicon python=3.12

conda activate deephelicon

Step 3: install via pip

Command

Log

cd deephelicon

pip install .

Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting biopython<2.0,>=1.85 (from deephelicon==0.0.1)
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Requirement already satisfied: setuptools in d:\programming\anaconda3\envs\deephelicon\lib\site-packages (from tensorflow==2.19->deephelicon==0.0.1) (78.1.0)
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Collecting charset-normalizer<4,>=2 (from requests<3,>=2.21.0->tensorflow==2.19->deephelicon==0.0.1)
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Collecting idna<4,>=2.5 (from requests<3,>=2.21.0->tensorflow==2.19->deephelicon==0.0.1)
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Collecting certifi>=2017.4.17 (from requests<3,>=2.21.0->tensorflow==2.19->deephelicon==0.0.1)
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Collecting markdown>=2.6.8 (from tensorboard~=2.19.0->tensorflow==2.19->deephelicon==0.0.1)
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Collecting MarkupSafe>=2.1.1 (from werkzeug>=1.0.1->tensorboard~=2.19.0->tensorflow==2.19->deephelicon==0.0.1)
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Building wheels for collected packages: deephelicon
  Building wheel for deephelicon (pyproject.toml) ... done
  Created wheel for deephelicon: filename=deephelicon-0.0.1-py3-none-any.whl size=43805 sha256=737164dfce4079656dc6e962546a53d8ef1d5d1a79f1718fe0b36417c4d885d6
  Stored in directory: C:\Users\jianf\AppData\Local\Temp\pip-ephem-wheel-cache-1tmt2fi6\wheels\79\7b\16\b43d9771719ae42acfe1e86d8a33d0f8e7b50801f3f0b2b0bc
Successfully built deephelicon
Installing collected packages: pytz, namex, libclang, flatbuffers, wrapt, urllib3, tzdata, typing-extensions, termcolor, tensorboard-data-server, six, pygments, pyfiglet, protobuf, packaging, opt-einsum, numpy, mdurl, MarkupSafe, markdown, llvmlite, joblib, idna, grpcio, gast, colorama, charset-normalizer, certifi, absl-py, werkzeug, requests, python-dateutil, optree, numba, ml-dtypes, markdown-it-py, h5py, google-pasta, click, biopython, astunparse, tensorboard, rich, pandas, keras, tensorflow, deephelicon
Successfully installed MarkupSafe-3.0.2 absl-py-2.2.2 astunparse-1.6.3 biopython-1.85 certifi-2025.1.31 charset-normalizer-3.4.1 click-8.1.8 colorama-0.4.6 deephelicon-0.0.1 flatbuffers-25.2.10 gast-0.6.0 google-pasta-0.2.0 grpcio-1.71.0 h5py-3.13.0 idna-3.10 joblib-1.4.2 keras-3.9.2 libclang-18.1.1 llvmlite-0.44.0 markdown-3.7 markdown-it-py-3.0.0 mdurl-0.1.2 ml-dtypes-0.5.1 namex-0.0.8 numba-0.61.0 numpy-2.1.3 opt-einsum-3.4.0 optree-0.14.1 packaging-24.2 pandas-2.2.3 protobuf-5.29.4 pyfiglet-1.0.2 pygments-2.19.1 python-dateutil-2.9.0.post0 pytz-2025.2 requests-2.32.3 rich-14.0.0 six-1.17.0 tensorboard-2.19.0 tensorboard-data-server-0.7.2 tensorflow-2.19.0 termcolor-3.0.1 typing-extensions-4.13.1 tzdata-2025.2 urllib3-2.3.0 werkzeug-3.1.3 wrapt-1.17.2

Everything should be all set before you run DeepHelicon.