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Dockerfile
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FROM ubuntu:bionic
LABEL maintainer="Contextual Dynamics Lab <[email protected]>"
ARG DEBIAN_FRONTEND=noninteractive
ARG WORKDIR="/mnt"
ARG NOTEBOOK_IP=0.0.0.0
ARG PORT=9999
ENV LANG=C.UTF-8 \
PATH="/opt/conda/bin:$PATH" \
NOTEBOOK_DIR=$WORKDIR \
NOTEBOOK_IP=$NOTEBOOK_IP \
NOTEBOOK_PORT=$PORT
SHELL ["/bin/bash", "-o", "pipefail", "-c"]
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc \
&& apt-get update --fix-missing \
&& apt-get install -y --no-install-recommends eatmydata \
&& eatmydata apt-get install -y --no-install-recommends \
bzip2 \
ca-certificates \
curl \
gcc \
git \
libfontconfig1-dev \
libgl1-mesa-glx -y \
mpich \
pkg-config \
sudo \
swig \
vim \
wget \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh -O ~/miniconda.sh \
&& /bin/bash ~/miniconda.sh -b -p /opt/conda \
&& rm ~/miniconda.sh \
&& conda config --set auto_update_conda false \
&& conda config --set notify_outdated_conda false \
&& conda install -y \
_libgcc_mutex=0.1=main \
blas=1.0=mkl \
ca-certificates=2019.5.15=1 \
certifi=2019.6.16=py36_1 \
ipykernel=5.3.4 \
ipython=7.16.1 \
ipywidgets=7.5.1 \
jinja2=2.11.2 \
libedit=3.1.20181209=hc058e9b_0 \
libffi=3.2.1=hd88cf55_4 \
libgcc-ng=8.2.0=hdf63c60_1 \
libgfortran-ng=7.3.0=hdf63c60_0 \
libstdcxx-ng=8.2.0=hdf63c60_1 \
mkl-service=2.0.2=py36h7b6447c_0 \
mkl_fft=1.0.12=py36ha843d7b_0 \
mkl_random=1.0.2=py36hd81dba3_0 \
nbconvert=5.6.1 \
nbformat=5.0.7 \
ncurses=6.1=he6710b0_1 \
notebook=6.1.4 \
numpy-base=1.16.4=py36hde5b4d6_0 \
openssl=1.1.1c=h7b6447c_1 \
pandoc=2.10 \
pip=19.0.3=py36_0 \
prometheus_client=0.8.0 \
python=3.6.8=h0371630_0 \
pyzmq=19.0.2 \
readline=7.0=h7b6447c_5 \
setuptools=40.8.0=py36_0 \
sqlite=3.27.2=h7b6447c_0 \
terminado=0.9.1 \
tk=8.6.8=hbc83047_0 \
tornado=6.0.4 \
traitlets=4.3.3 \
wheel=0.33.1=py36_0 \
widgetsnbextension=3.5.1 \
xz=5.2.4=h14c3975_4 \
zlib=1.2.11=h7b6447c_3 \
&& conda clean -tipsy \
&& pip install \
alabaster==0.7.12 \
babel==2.6.0 \
biopython==1.74 \
chardet==3.0.4 \
citeproc-py==0.4.0 \
cycler==0.10.0 \
deepdish==0.3.6 \
docutils==0.14 \
duecredit==0.7.0 \
future==0.17.1 \
hypertools==0.5.1 \
idna==2.8 \
imagesize==1.1.0 \
intel-openmp==2019.0 \
jinja2==2.10 \
jupyter_contrib_nbextensions==0.5.1 \
kiwisolver==1.0.1 \
llvmlite==0.28.0 \
lxml==4.3.3 \
markupsafe==1.1.1 \
matplotlib==3.0.3 \
mkl==2019.0 \
mock==2.0.0 \
neurosynth==0.3.8 \
nibabel==2.5.0 \
nose==1.3.7 \
numba==0.43.1 \
numexpr==2.6.9 \
numpy==1.16.2 \
packaging==19.0 \
pandas==0.24.2 \
pbr==5.1.3 \
ply==3.11 \
ppca==0.0.4 \
pygments==2.3.1 \
pyparsing==2.3.1 \
python-dateutil==2.8.0 \
pytz==2018.9 \
requests==2.21.0 \
scikit-learn==0.19.2 \
scipy==1.2.1 \
seaborn==0.9.0 \
six==1.12.0 \
snowballstemmer==1.2.1 \
sphinx==2.0.0 \
sphinxcontrib-applehelp==1.0.1 \
sphinxcontrib-devhelp==1.0.1 \
sphinxcontrib-htmlhelp==1.0.1 \
sphinxcontrib-jsmath==1.0.1 \
sphinxcontrib-qthelp==1.0.2 \
sphinxcontrib-serializinghtml==1.1.3 \
tables==3.5.1 \
umap-learn==0.3.8 \
urllib3==1.24.1 \
git+git://github.com/lucywowen/timecorr-1.git@spot_check \
git+https://github.com/FIU-Neuro/brainconn.git \
&& rm -rf ~/.cache/pip \
&& jupyter nbextension enable --py widgetsnbextension --sys-prefix \
&& jupyter notebook --generate-config \
&& ipython profile create \
&& sed -i \
-e 's/^# c.Completer.use_jedi = True/c.Completer.use_jedi = False/' \
-e 's/^#c.Completer.use_jedi = True/c.Completer.use_jedi = False/' \
-e 's/^# c.IPCompleter.use_jedi = True/c.IPCompleter.use_jedi = False/' \
~/.ipython/profile_default/ipython_config.py \
&& mkdir -p /root/.jupyter \
&& echo "from os import getenv" > /root/.jupyter/jupyter_notebook_config.py \
&& echo "c.NotebookApp.ip = getenv(\"NOTEBOOK_IP\")" >> /root/.jupyter/jupyter_notebook_config.py \
&& echo "c.NotebookApp.port = int(getenv(\"NOTEBOOK_PORT\"))" >> /root/.jupyter/jupyter_notebook_config.py \
&& echo "c.NotebookApp.notebook_dir = getenv(\"NOTEBOOK_DIR\")" >> /root/.jupyter/jupyter_notebook_config.py \
&& echo "c.NotebookApp.open_browser = False" >> /root/.jupyter/jupyter_notebook_config.py \
&& echo "c.NotebookApp.allow_root = True" >> /root/.jupyter/jupyter_notebook_config.py \
&& echo "c.FileContentsManager.delete_to_trash = False" >> /root/.jupyter/jupyter_notebook_config.py
WORKDIR $WORKDIR