Merge pull request #124 from hydroshare/develop

Longstanding changes in develop

Author: Castronova

docker/Dockerfile

@@ -1,129 +1,10 @@
-FROM castrona/hydroshare-jupyterhub:latest
+FROM castrona/hydroshare-jupyterhub:1.3
 MAINTAINER Tony Castronova <acastronova@cuahsi.org>
 
 ######################################################
 ### Begin - JupyterHub Development Image Additions ###
 ######################################################
 
-USER root
-
-RUN apt-get update -y
-RUN apt-get install -y libx11-dev
-
-# NBExtensions
-RUN git clone https://github.com/Castronova/jupyter_contrib_nbextensions.git /home/jovyan/libs/jupyter_contrib_nbextensions
-RUN pip3 install -e /home/jovyan/libs/jupyter_contrib_nbextensions
-RUN jupyter contrib nbextension install --system
-RUN jupyter nbextension enable recursivedelete/main --user --section=tree
-RUN jupyter nbextensions_configurator disable --user
-RUN chown -R jovyan:users /home/jovyan/.jupyter
-
-ENV NOTEBOOK_HOME=/home/jovyan/work/notebooks
-ENV PATH=$PATH:/home/jovyan/libs/DHSVM-PNNL/DHSVM/sourcecode
-
-USER jovyan
-
-RUN pip install wget
-RUN pip3 install wget 
-RUN pip install ulmo
-
-# patch hs_restclient v1.2.6 
-ADD docker/hs_restclient.patch /home/jovyan/libs/hs_restclient/hs_restclient/hs_restclient.patch
-RUN cd /home/jovyan/libs/hs_restclient/hs_restclient && patch < hs_restclient.patch
-
-# install DHSVM (need to modify UFconfig.mk for linux)
-RUN git clone -b glacier https://github.com/pnnl/DHSVM-PNNL.git /home/jovyan/libs/DHSVM-PNNL
-RUN sed -i '/# CC = gcc/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
-RUN sed -i '/# CFLAGS = -O3 -fexceptions/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
-RUN sed -i '/# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread/s/^# //' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
-RUN sed -i 's/F77 = gfortran/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
-RUN sed -i 's/CFLAGS = -O3 -fno-common -no-cpp-precomp -fexception/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
-RUN sed -i 's/BLAS = -framework Accelerate/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
-RUN sed -i 's/LAPACK = -framework Accelerate/# &/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/UFconfig/UFconfig.mk
-RUN sed -i 's/DEFS =  -DHAVE_X11 -DHAVE_GLACIER/DEFS =  -DHAVE_X11/' /home/jovyan/libs/DHSVM-PNNL/DHSVM/sourcecode/makefile
-RUN rm /home/jovyan/libs/DHSVM-PNNL/DHSVM/Lib/libcxsparse.a
-RUN cd /home/jovyan/libs/DHSVM-PNNL/DHSVM/Lib && make
-RUN cd /home/jovyan/libs/DHSVM-PNNL/DHSVM/sourcecode && make 
-
-# install Boost and Dakota
-RUN wget -O /home/jovyan/libs/boost.tar.gz https://sourceforge.net/projects/boost/files/boost/1.53.0/boost_1_53_0.tar.gz/download
-RUN mkdir /home/jovyan/libs/boost && tar xzfv /home/jovyan/libs/boost.tar.gz -C /home/jovyan/libs/boost --strip-components 1
-
-  ###### BEGIN ROOT #######
-  USER root
-  
-  RUN cd /home/jovyan/libs/boost && ./bootstrap.sh --prefix=/usr/local
-  RUN echo "using mpi ;" >> /home/jovyan/libs/boost/tools/build/v2/user-config.jam
-  RUN cd /home/jovyan/libs/boost && ./b2 --with=all -j 4 install; exit 0
-  RUN sh -c 'echo "/usr/local/lib" >> /etc/ld.so.conf.d/local.conf'
-  RUN ldconfig
-  RUN apt-get install -y libblas-dev liblapack-dev cmake
-  
-  USER jovyan
-  ####### END ROOT ########
-
-RUN wget https://dakota.sandia.gov/sites/default/files/distributions/public/dakota-6.5-public.src.tar.gz -P /home/jovyan/libs
-RUN tar xzf /home/jovyan/libs/dakota-6.5-public.src.tar.gz -C /home/jovyan/libs
-RUN mkdir /home/jovyan/libs/dakota-6.5.0.src/build
-ADD docker/dakota_template.cmake /home/jovyan/libs/dakota-6.5.0.src/build/BuildDakota.cmake
-RUN cd /home/jovyan/libs/dakota*.src/build && cmake -C BuildDakota.cmake /home/jovyan/libs/dakota*.src
-
-  ###### BEGIN ROOT #######
-  USER root
-  RUN cd /home/jovyan/libs/dakota*.src/build && make clean
-  RUN cd /home/jovyan/libs/dakota*.src/build && make
-  RUN cd /home/jovyan/libs/dakota*.src/build && make install
-  ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
-  USER jovyan
-  ####### END ROOT ########
-
-ADD docker/icommands.sh /home/jovyan/libs/icommands.sh 
-USER root
-RUN chmod +x /home/jovyan/libs/icommands.sh
-RUN echo "/home/jovyan/libs" | /home/jovyan/libs/icommands.sh
-USER jovyan
-
-ENV \
-PATH=/home/jovyan/libs/icommands:$PATH \
-IRODS_PLUGINS_HOME=/home/jovyan/libs/icommands/plugins/ \
-IRODS_ENVIRONMENT_FILE=/home/jovyan/work/notebooks/data/.irods/irods_environment.json \ 
-IRODS_AUTHENTICATION_FILE=/home/jovyan/work/notebooks/data/.irods/.irodsA
-
-RUN pip install git+https://github.com/cybergis/jupyterlib.git
-RUN pip3 install git+https://github.com/cybergis/jupyterlib.git
-
-  ###### BEGIN ROOT #######
-  USER root
-
-  # register the kernel in the current R installation
-  RUN sh -c 'echo "deb http://cran.rstudio.com/bin/linux/debian jessie-cran3/" >> /etc/apt/sources.list'
-  RUN gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
-  RUN gpg -a --export E084DAB9 | apt-key add -
-  RUN apt-key update
-  RUN apt-get update
-  
-  # required libs for installing R packages
-  RUN apt-get -y install \
-      libcurl4-openssl-dev \
-      libssl-dev \
-      make \
-      gcc \
-      g++
-  
-  # install R-base packages (including IRKernel)
-  RUN apt-get install --allow-unauthenticated --no-install-recommends -y r-base=3.3*
-  RUN Rscript -e "install.packages('devtools', repos='http://archive.linux.duke.edu/cran')"
-  RUN Rscript -e "devtools::install_github('IRkernel/IRkernel')"
-  USER jovyan
-  ####### END ROOT ########
-
-RUN Rscript -e "IRkernel::installspec(name = 'ir33', displayname = 'R 3.3')"
-
-RUN pip install geopandas
-RUN pip3 install geopandas
-
-RUN pip install graphviz
-RUN pip3 install graphviz
 
 ###################################################
 ## End - JupyterHub Development Image Additions ###