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jgould
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FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:0.0.9 | ||
USER root | ||
#this makes it so pip runs as root, not the user | ||
ENV PIP_USER=false | ||
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RUN apt-get update && apt-get install -yq --no-install-recommends \ | ||
build-essential \ | ||
automake \ | ||
zlib1g-dev \ | ||
libxml2-dev \ | ||
cmake \ | ||
python3.7-dev \ | ||
gnupg \ | ||
lsb-release \ | ||
libfftw3-dev \ | ||
default-jdk && \ | ||
apt-get clean && \ | ||
rm -rf /var/lib/apt/lists/* | ||
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RUN pip3 -V && \ | ||
pip3 install --upgrade pip && \ | ||
pip3 install numpy==1.18.2 && \ | ||
pip3 install Cython==0.29.16 && \ | ||
pip3 install pybind11==2.4.3 && \ | ||
pip3 install h5py==2.10.0 && \ | ||
pip3 install fitsne==1.1.1 && \ | ||
pip3 install joblib==0.14.1 && \ | ||
pip3 install leidenalg==0.7.0 && \ | ||
pip3 install lightgbm==2.2.1 && \ | ||
pip3 install llvmlite==0.31.0 && \ | ||
pip3 install loompy==3.0.6 && \ | ||
pip3 install natsort==7.0.1 && \ | ||
pip3 install numba==0.48.0 && \ | ||
pip3 install pandas==1.0.1 && \ | ||
pip3 install scikit-learn==0.22.2.post1 && \ | ||
pip3 install scikit-misc==0.1.1 && \ | ||
pip3 install scipy==1.4.1 && \ | ||
pip3 install statsmodels==0.11.1 && \ | ||
pip3 install tables==3.6.1 && \ | ||
pip3 install torch==1.4.0 && \ | ||
pip3 install anndata==0.7.1 && \ | ||
pip3 install harmony-pytorch==0.1.3 && \ | ||
pip3 install hnswlib==0.3.4 && \ | ||
pip3 install fisher==0.1.9 && \ | ||
pip3 install python-igraph==0.7.1.post6 && \ | ||
pip3 install louvain-github==0.6.1.post1 && \ | ||
pip3 install MulticoreTSNE-modified==0.1 && \ | ||
pip3 install umap-learn==0.3.10 && \ | ||
pip3 install bokeh==2.0.0 && \ | ||
pip3 install scplot==0.0.16 && \ | ||
pip3 install pegasuspy==0.17.1 && \ | ||
pip3 install wot==1.0.8.post1 | ||
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ENV USER jupyter-user | ||
USER $USER | ||
#we want pip to install into the user's dir when the notebook is running | ||
ENV PIP_USER=true | ||
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ENTRYPOINT ["/usr/local/bin/jupyter", "notebook"] |
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#!/usr/bin/env bash | ||
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docker build -t wot-terra-1.0.8.post1 . | ||
docker tag wot-terra-1.0.8.post1 klarmancellobservatory/wot-terra:1.0.8.post1 | ||
docker push klarmancellobservatory/wot-terra:1.0.8.post1 |