diff --git a/docker/Dockerfile b/docker/Dockerfile new file mode 100644 index 0000000..a7d8dc4 --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1,22 @@ +FROM continuumio/anaconda3 + +USER root + +RUN apt-get -y update && apt install -y build-essential + +COPY spec-list.pathflow.txt . + +RUN conda create --name default --file spec-list.pathflow.txt && \ + rm spec-list.pathflow.txt + +COPY requirements.txt . + +RUN pip install -r requirements.txt && \ + rm requirements.txt + +RUN pip install git+https://github.com/jlevy44/PathFlowAI.git + +RUN install_apex + +ENTRYPOINT [ "/usr/bin/tini", "--" ] +CMD [ "/bin/bash" ] diff --git a/docker/requirements.txt b/docker/requirements.txt new file mode 100644 index 0000000..1997da6 --- /dev/null +++ b/docker/requirements.txt @@ -0,0 +1,88 @@ +albumentations==0.4.1 +asciitree==0.3.3 +beautifulsoup4==4.8.1 +blosc==1.8.1 +brambox==2.1.0 +certifi==2019.9.11 +chardet==3.0.4 +click==6.7 +cloudpickle==1.2.2 +cycler==0.10.0 +dask==2.6.0 +dask-image==0.2.0 +decorator==4.4.0 +dill==0.3.1.1 +distributed==2.6.0 +efficientnet-pytorch==0.5.1 +fasteners==0.15 +fire==0.2.1 +fsspec==0.5.2 +future==0.18.1 +googledrivedownloader==0.4 +GPUtil==1.4.0 +h5py==2.10.0 +HeapDict==1.0.1 +idna==2.8 +imageio==2.6.1 +imgaug==0.2.6 +isodate==0.6.0 +joblib==0.14.0 +kiwisolver==1.1.0 +locket==0.2.0 +matplotlib==3.1.1 +monotonic==1.5 +msgpack==0.6.2 +multiprocess==0.70.9 +networkx==2.4 +nonechucks==0.4.0 +nose==1.3.7 +numba==0.46.0 +numcodecs==0.6.3 +numpy==1.17.3 +opencv-python==4.1.1.26 +opencv-python-headless==4.1.1.26 +openslide-python==1.1.1 +pandas==0.25.0 +partd==1.0.0 +pathos==0.2.5 +Pillow==6.2.1 +PIMS==0.4.1 +plotly==4.2.1 +plyfile==0.7.1 +pox==0.2.7 +ppft==1.6.6.1 +progressbar2==3.47.0 +psutil==5.6.3 +pyparsing==2.4.2 +PySnooper==0.2.8 +python-dateutil==2.7.5 +python-utils==2.3.0 +pytz==2018.7 +PyWavelets==1.1.1 +rdflib==4.2.2 +requests==2.22.0 +retrying==1.3.3 +scikit-image==0.16.2 +scikit-learn==0.21.3 +scipy==1.3.1 +seaborn==0.9.0 +shap==0.31.0 +Shapely==1.6.4.post2 +six==1.12.0 +slicerator==1.0.0 +sortedcontainers==2.1.0 +soupsieve==1.9.4 +tblib==1.5.0 +termcolor==1.1.0 +tifffile==2019.7.26 +toolz==0.10.0 +torch==1.3.0 +torch-encoding==1.0.1 +torchvision==0.4.1 +tornado==6.0.3 +tqdm==4.36.1 +umap-learn==0.3.10 +urllib3==1.25.6 +xarray==0.14.0 +zarr==2.3.2 +zict==1.0.0 diff --git a/docker/spec-list.pathflow.txt b/docker/spec-list.pathflow.txt new file mode 100644 index 0000000..718714b --- /dev/null +++ b/docker/spec-list.pathflow.txt @@ -0,0 +1,61 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda +https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.31.1-h7fc9f1b_2.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2019.9.11-hecc5488_0.tar.bz2 +https://repo.anaconda.com/pkgs/main/linux-64/libstdcxx-ng-9.1.0-hdf63c60_0.conda +https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.31.1-h6176602_12.tar.bz2 +https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-9.1.0-hdf63c60_0.conda +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h516909a_1.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/icu-64.2-he1b5a44_1.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/jpeg-9c-h14c3975_1001.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.2.1-he1b5a44_1006.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-7.2.0-h69d50b8_2.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.15-h516909a_1005.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h14c3975_1000.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.8.3-he1b5a44_1001.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.1-hf484d3e_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1c-h516909a_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/pcre-8.43-he1b5a44_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/pixman-0.38.0-h516909a_1003.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h14c3975_1001.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h14c3975_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.0.10-h516909a_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.9-h14c3975_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h516909a_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h14c3975_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h14c3975_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h14c3975_1007.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.4-h14c3975_1001.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.11-h516909a_1006.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/gcc_linux-64-7.3.0-h553295d_12.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.8.1-hc5be6a0_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20170329-hf8c457e_1001.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.37-hed695b0_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h14c3975_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.9.9-hee79883_5.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.0-hf8c457e_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.9-hed695b0_1003.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.3-h84519dc_1000.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.4.3-h3b9ef0a_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/freetype-2.10.0-he983fc9_1.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/glib-2.58.3-h6f030ca_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/gxx_linux-64-7.3.0-h553295d_12.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.0.10-hfc65ed5_1004.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.30.1-hcee41ef_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.6.9-h516909a_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.13.1-h86ecdb6_1001.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.3.1-h21c5421_1.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/python-3.7.3-h33d41f4_1.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h516909a_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.10-h516909a_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/cairo-1.16.0-hfb77d84_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/certifi-2019.9.11-py37_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/gobject-introspection-1.58.2-py37h5503ade_1002.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/setuptools-41.4.0-py37_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.36.12-h7a26e22_1003.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/wheel-0.33.6-py37_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/openslide-3.4.1-h8137273_0.tar.bz2 +https://conda.anaconda.org/conda-forge/linux-64/pip-19.3.1-py37_0.tar.bz2