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Merge pull request #139 from AlexandrovLab/container
Add Docker Container
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# Start with a base Ubuntu image and install Python | ||
FROM ubuntu:22.04 | ||
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# Avoid prompts from apt | ||
ARG DEBIAN_FRONTEND=noninteractive | ||
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# Install Python and other dependencies, and apply updates | ||
RUN apt-get update && apt-get upgrade -y && \ | ||
apt-get install -y python3-pip python3-dev git && \ | ||
apt-get clean && rm -rf /var/lib/apt/lists/* | ||
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# Set the working directory in the container | ||
WORKDIR /usr/src/app | ||
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# Clone the specific branch of the repository | ||
RUN git clone https://github.com/AlexandrovLab/SigProfilerAssignment.git . | ||
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# Install the dependencies from the requirements.txt in the cloned repository | ||
RUN pip3 install --no-cache-dir -r requirements.txt | ||
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# Install the SigProfilerAssignment package from PyPI | ||
RUN pip3 install SigProfilerAssignment==0.1.8 | ||
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# Create a non-root user named 'spm_user' | ||
RUN useradd -m -s /bin/bash spm_user | ||
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# Change the ownership of the /usr/src/app directory and its contents to the new non-root user | ||
RUN chown -R spm_user:spm_user /usr/src/app | ||
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# Switch to the non-root user for subsequent commands and when running the container | ||
USER spm_user |
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Original file line number | Diff line number | Diff line change |
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scipy | ||
numpy | ||
pandas | ||
SigProfilerMatrixGenerator | ||
sigProfilerPlotting | ||
pillow | ||
statsmodels | ||
scikit-learn | ||
psutil | ||
reportlab | ||
pypdf | ||
alive_progress | ||
# | ||
# This file is autogenerated by pip-compile with Python 3.11 | ||
# by the following command: | ||
# | ||
# pip-compile setup.py | ||
# | ||
about-time==4.2.1 | ||
# via alive-progress | ||
alive-progress==3.1.5 | ||
# via SigProfilerAssignment (setup.py) | ||
chardet==5.2.0 | ||
# via reportlab | ||
contourpy==1.2.1 | ||
# via matplotlib | ||
cycler==0.12.1 | ||
# via matplotlib | ||
fonttools==4.53.1 | ||
# via matplotlib | ||
grapheme==0.6.0 | ||
# via alive-progress | ||
joblib==1.4.2 | ||
# via scikit-learn | ||
kiwisolver==1.4.5 | ||
# via matplotlib | ||
matplotlib==3.9.2 | ||
# via | ||
# sigprofilermatrixgenerator | ||
# sigprofilerplotting | ||
numpy==1.26.4 | ||
# via | ||
# SigProfilerAssignment (setup.py) | ||
# contourpy | ||
# matplotlib | ||
# pandas | ||
# patsy | ||
# scikit-learn | ||
# scipy | ||
# sigprofilermatrixgenerator | ||
# statsmodels | ||
packaging==24.1 | ||
# via | ||
# matplotlib | ||
# statsmodels | ||
pandas==1.5.3 | ||
# via | ||
# SigProfilerAssignment (setup.py) | ||
# sigprofilermatrixgenerator | ||
# sigprofilerplotting | ||
# statsmodels | ||
patsy==0.5.6 | ||
# via statsmodels | ||
pillow==10.4.0 | ||
# via | ||
# matplotlib | ||
# reportlab | ||
# sigprofilerplotting | ||
pymupdf==1.24.9 | ||
# via SigProfilerAssignment (setup.py) | ||
pymupdfb==1.24.9 | ||
# via pymupdf | ||
pyparsing==3.1.2 | ||
# via matplotlib | ||
pypdf==4.3.1 | ||
# via SigProfilerAssignment (setup.py) | ||
python-dateutil==2.9.0.post0 | ||
# via | ||
# matplotlib | ||
# pandas | ||
pytz==2024.1 | ||
# via pandas | ||
reportlab==4.2.2 | ||
# via SigProfilerAssignment (setup.py) | ||
scikit-learn==1.5.1 | ||
# via sigprofilerplotting | ||
scipy==1.14.0 | ||
# via | ||
# SigProfilerAssignment (setup.py) | ||
# scikit-learn | ||
# sigprofilermatrixgenerator | ||
# statsmodels | ||
sigprofilermatrixgenerator==1.2.28 | ||
# via SigProfilerAssignment (setup.py) | ||
sigprofilerplotting==1.3.24 | ||
# via | ||
# SigProfilerAssignment (setup.py) | ||
# sigprofilermatrixgenerator | ||
six==1.16.0 | ||
# via | ||
# patsy | ||
# python-dateutil | ||
statsmodels==0.14.2 | ||
# via sigprofilermatrixgenerator | ||
threadpoolctl==3.5.0 | ||
# via scikit-learn |
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