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Merged
jlevy44 merged 3 commits into from
Mar 22, 2020
Merged

Dockerfile #11

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6205770
First attempt at docker.. Need nvidia-docker and singularity
jlevy44 Mar 16, 2020
5a94eb1
Updates to dockerfile
jlevy44 Mar 22, 2020
7ce1a63
changed capitalization of docker
jlevy44 Mar 22, 2020
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22 changes: 22 additions & 0 deletions docker/Dockerfile
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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" ]
88 changes: 88 additions & 0 deletions docker/requirements.txt
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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
61 changes: 61 additions & 0 deletions docker/spec-list.pathflow.txt
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# This file may be used to create an environment using:
# $ conda create --name <env> --file <this 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