Merge pull request #29 from hydroshare/develop

Release 1.0
hydroshare · Dec 9, 2016 · bcb3c3b · bcb3c3b
2 parents 3adc66f + 867cb7c
commit bcb3c3b
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diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,153 +1,14 @@
-# Build as jupyterhub/singleuser
-# Run with the DockerSpawner in JupyterHub
+FROM castrona/hydroshare-jupyterhub:latest
+MAINTAINER Tony Castronova <[email protected]>
 
-# Minimal Jupyter Notebook Stack comes with: 
-# Jupyter Notebook 4.2.x
-# Conda Python 3.x
-# No preinstalled scientific computing packages
-# Unprivileged user jovyan (uid=1000, configurable, see options) in group users (gid=100) with ownership over /home/jovyan and /opt/conda
-# tini as the container entrypoint and start-notebook.sh as the default command
-# A start-singleuser.sh script for use as an alternate command that runs a single-user instance of the Notebook server, as required by JupyterHub
-# Options for HTTPS, password auth, and passwordless sudo
+######################################################
+### Begin - JupyterHub Development Image Additions ###
+######################################################
 
 
-FROM jupyter/scipy-notebook
-
-MAINTAINER Tony Castronova <[email protected]>
-
-EXPOSE 8888
-
-USER root
-
-############################
-# INSTALL SYSTEM LIBRARIES #
-############################
-
-# libgeos-dev RHESYSS dependency
-# mpic++ TAUDEM dependency
-# libgdal-dev TAUDEM dependency
-# libproj-dev TAUDEM dependency
-RUN apt-get clean && apt-get update --fix-missing
-
-RUN apt-get install -y libgeos-dev mpic++ libproj-dev 
-
-# install irods fuse
-RUN apt-get install -y fuse libfuse2 libfuse-dev
-RUN wget -q ftp://ftp.renci.org/pub/irods/releases/4.1.8/ubuntu12/irods-icommands-4.1.8-ubuntu12-x86_64.deb -O /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
-RUN dpkg -i /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
-RUN groupadd fuse && usermod -aG fuse jovyan
-RUN chmod g+rw /dev/fuse && chgrp fuse /dev/fuse
-
-# install rhessys workflows
-RUN apt-get install -y build-essential git subversion p7zip-full python python-dev python-pip python-scipy libxml2-dev libxslt-dev libgdal-dev libgdal-doc gdal-bin python-gdal grass grass-dev libbsd-dev vlc 
-
-# create directories
-RUN mkdir /home/jovyan/libs && chown -R jovyan:users /home/jovyan/libs
-RUN mkdir /home/jovyan/work/notebooks && chown -R jovyan:users /home/jovyan/work/notebooks
-#RUN mkdir /home/jovyan/grassdata && chown -R jovyan:users /home/jovyan/grassdata
-
-###############################
-# SETUP JUPYTERHUB ENTRYPOINT #
-###############################
-
-# fetch juptyerhub-singleuser entrypoint
-RUN wget -q https://raw.githubusercontent.com/jupyterhub/jupyterhub/master/scripts/jupyterhub-singleuser -O /usr/local/bin/jupyterhub-singleuser && \
- chmod 755 /usr/local/bin/jupyterhub-singleuser
-ADD singleuser.sh /srv/singleuser/singleuser.sh
-
-# add grass create location script
-#RUN chmod 755 /home/jovyan/libs/create_grass_loc.sh && chown jovyan:users /home/jovyan/libs/create_grass_loc.sh
-
-# fetch the ecohydro config file
-ADD https://raw.github.com/selimnairb/RHESSysWorkflows/master/docs/config/ecohydro-Linux.cfg /home/jovyan/.ecohydro.cfg 
-RUN chown jovyan:users /home/jovyan/.ecohydro.cfg
-
-##################
-# PREPARE TAUDEM #
-##################
-
-# install taudem (must happend before rhesyss b/c of gdal conflicts)
-RUN git clone https://github.com/dtarb/TauDEM.git ../libs/TauDEM && \
-cd ../libs/TauDEM/src && make 
-
-# link conda python2 (used by jupyterhub) to python22
-RUN ln -s /opt/conda/envs/python2/bin/python2 /usr/bin/python22
-
-# prepare grass
-#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
-#RUN chown jovyan:users /home/jovyan/libs/create_grass_loc.sh && \
-#chmod +x /home/jovyan/libs/create_grass_loc.sh
-
-#########################
-# SWITCH TO JOVYAN USER #
-#########################
-USER jovyan 
-
-# load the rhessys configuration file
-RUN sed -i -e 's|^ETC.*|ETC = /home/jovyan/libs/RHESSysWorkflows/etc|g' /home/jovyan/.ecohydro.cfg &&\
-sed -i -e 's|^MODULE_PATH.*|MODULE_PATH = /home/jovyan/work/notebooks/.grass6/addons|g' /home/jovyan/.ecohydro.cfg &&\
-sed -i -e 's|^MODULE_ETC.*|MODULE_ETC = /home/jovyan/libs/RHESSysWorkflows/etc/r.soils.texture|g' /home/jovyan/.ecohydro.cfg
-
-# prepare python environments
-RUN pip install --upgrade pip
-
-# install ecohydrolib
-RUN git clone https://github.com/leonard-psu/EcohydroLib.git ../libs/EcohydroLib
-RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
-&& cd ../libs/EcohydroLib \
-&& python setup.py install "
-
-# install RHESSysWorkflows
-RUN git clone https://github.com/leonard-psu/RHESSysWorkflows.git ../libs/RHESSysWorkflows
-RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
-&& cd ../libs/RHESSysWorkflows \
-&& python setup.py install"
-
-RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
-&& pip install --upgrade pip \
-&& pip install wget "
-
-###############################
-# PREPARE PYTHON ENVIRONMENTS #
-###############################
-
-# Python 3
-RUN conda install -y -n root \
-gdal \
-basemap \
-landlab -c landlab
-
-RUN git clone -b 2_and_3 https://github.com/hydroshare/hs_restclient.git ../libs/hs_restclient
-RUN /bin/bash -c "source /opt/conda/bin/activate root \
-&& cd ../libs/hs_restclient \
-&& python setup.py install "
-
-# Python 2
-# install gdal into python2 conda env
-RUN conda install -y -n python2 \
-gdal \
-basemap \
-landlab -c landlab 
-
-######################
-# SET PATH VARIABLES #
-######################
-
-ENV PATH=/opt/conda/envs/python2/bin:/home/jovyan/libs/TauDEM:$PATH PYTHONPATH=/home/jovyan/work/notebooks/utilities:$PYTHONPATH DOCUMENTS=/home/jovyan/work/notebooks/documents DATA=/home/jovyan/work/notebooks/data HOME=/home/jovyan/work/notebooks ECOHYDROLIB_CFG=/home/jovyan/.ecohydro.cfg LD_LIBRARY_PATH=/usr/lib/grass64/lib
-
-#RUN /bin/bash -c "source /opt/conda/bin/activate python2" && \
-#pip install --upgrade hs_restclient
-
-# install odm2api, then upgrade it to renamevalueobjects branch
-RUN conda install -y -n python2 -c odm2 odm2api
-RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
-&& pip install --upgrade --process-dependency-links git+https://github.com/ODM2/ODM2PythonAPI.git@renamevalueobjects"
-
-# prepare grass environment
-#RUN mkdir notebooks
-#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
-ADD rhessys_wf.py /home/jovyan/libs/rhessys_wf.py
-ADD run.py /home/jovyan/libs/run.py
+###################################################
+## End - JupyterHub Development Image Additions ###
+###################################################
 
 CMD ["sh", "/srv/singleuser/singleuser.sh"]
 

diff --git a/docker/__init__.py b/docker/__init__.py
diff --git a/docker/bck/Dockerfile b/docker/bck/Dockerfile
@@ -0,0 +1,155 @@
+# Build as jupyterhub/singleuser
+# Run with the DockerSpawner in JupyterHub
+
+# Minimal Jupyter Notebook Stack comes with: 
+# Jupyter Notebook 4.2.x
+# Conda Python 3.x
+# No preinstalled scientific computing packages
+# Unprivileged user jovyan (uid=1000, configurable, see options) in group users (gid=100) with ownership over /home/jovyan and /opt/conda
+# tini as the container entrypoint and start-notebook.sh as the default command
+# A start-singleuser.sh script for use as an alternate command that runs a single-user instance of the Notebook server, as required by JupyterHub
+# Options for HTTPS, password auth, and passwordless sudo
+
+
+FROM jupyter/scipy-notebook
+
+MAINTAINER Tony Castronova <[email protected]>
+
+EXPOSE 8888
+
+USER root
+
+############################
+# INSTALL SYSTEM LIBRARIES #
+############################
+
+# libgeos-dev RHESYSS dependency
+# mpic++ TAUDEM dependency
+# libgdal-dev TAUDEM dependency
+# libproj-dev TAUDEM dependency
+RUN apt-get clean && apt-get update --fix-missing
+
+RUN apt-get install -y libgeos-dev mpic++ libproj-dev 
+
+# install irods fuse
+RUN apt-get install -y fuse libfuse2 libfuse-dev
+RUN wget -q ftp://ftp.renci.org/pub/irods/releases/4.1.8/ubuntu12/irods-icommands-4.1.8-ubuntu12-x86_64.deb -O /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
+RUN dpkg -i /tmp/irods-icommands-4.1.8-ubuntu12-x86_64.deb
+RUN groupadd fuse && usermod -aG fuse jovyan
+RUN chmod g+rw /dev/fuse && chgrp fuse /dev/fuse
+
+# install rhessys workflows
+RUN apt-get install -y build-essential git subversion p7zip-full python python-dev python-pip python-scipy libxml2-dev libxslt-dev libgdal-dev libgdal-doc gdal-bin python-gdal grass grass-dev libbsd-dev vlc 
+
+# create directories
+RUN mkdir /home/jovyan/libs && chown -R jovyan:users /home/jovyan/libs
+RUN mkdir /home/jovyan/work/notebooks && chown -R jovyan:users /home/jovyan/work/notebooks
+#RUN mkdir /home/jovyan/grassdata && chown -R jovyan:users /home/jovyan/grassdata
+
+###############################
+# SETUP JUPYTERHUB ENTRYPOINT #
+###############################
+
+# fetch juptyerhub-singleuser entrypoint
+RUN wget -q https://raw.githubusercontent.com/jupyterhub/jupyterhub/master/scripts/jupyterhub-singleuser -O /usr/local/bin/jupyterhub-singleuser && \
+ chmod 755 /usr/local/bin/jupyterhub-singleuser
+ADD singleuser.sh /srv/singleuser/singleuser.sh
+
+# add grass create location script
+#RUN chmod 755 /home/jovyan/libs/create_grass_loc.sh && chown jovyan:users /home/jovyan/libs/create_grass_loc.sh
+
+# fetch the ecohydro config file
+ADD https://raw.github.com/selimnairb/RHESSysWorkflows/master/docs/config/ecohydro-Linux.cfg /home/jovyan/.ecohydro.cfg 
+RUN chown jovyan:users /home/jovyan/.ecohydro.cfg
+
+##################
+# PREPARE TAUDEM #
+##################
+
+# install taudem (must happend before rhesyss b/c of gdal conflicts)
+RUN git clone https://github.com/dtarb/TauDEM.git ../libs/TauDEM && \
+cd ../libs/TauDEM/src && make 
+
+# link conda python2 (used by jupyterhub) to python22
+RUN ln -s /opt/conda/envs/python2/bin/python2 /usr/bin/python22
+
+# prepare grass
+#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
+#RUN chown jovyan:users /home/jovyan/libs/create_grass_loc.sh && \
+#chmod +x /home/jovyan/libs/create_grass_loc.sh
+
+#########################
+# SWITCH TO JOVYAN USER #
+#########################
+USER jovyan 
+
+# load the rhessys configuration file
+RUN sed -i -e 's|^ETC.*|ETC = /home/jovyan/libs/RHESSysWorkflows/etc|g' /home/jovyan/.ecohydro.cfg &&\
+sed -i -e 's|^MODULE_PATH.*|MODULE_PATH = /home/jovyan/work/notebooks/.grass6/addons|g' /home/jovyan/.ecohydro.cfg &&\
+sed -i -e 's|^MODULE_ETC.*|MODULE_ETC = /home/jovyan/libs/RHESSysWorkflows/etc/r.soils.texture|g' /home/jovyan/.ecohydro.cfg
+
+# prepare python environments
+RUN pip install --upgrade pip
+
+# install ecohydrolib
+RUN git clone https://github.com/leonard-psu/EcohydroLib.git ../libs/EcohydroLib
+RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
+&& cd ../libs/EcohydroLib \
+&& python setup.py install "
+
+# install RHESSysWorkflows
+RUN git clone https://github.com/leonard-psu/RHESSysWorkflows.git ../libs/RHESSysWorkflows
+RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
+&& cd ../libs/RHESSysWorkflows \
+&& python setup.py install"
+
+RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
+&& pip install --upgrade pip \
+&& pip install wget "
+
+###############################
+# PREPARE PYTHON ENVIRONMENTS #
+###############################
+
+# Python 3
+RUN conda install -y -n root \
+gdal \
+basemap \
+landlab -c landlab
+
+RUN git clone -b 2_and_3 https://github.com/hydroshare/hs_restclient.git ../libs/hs_restclient
+RUN /bin/bash -c "source /opt/conda/bin/activate root \
+&& cd ../libs/hs_restclient \
+&& python setup.py install "
+
+# Python 2
+# install gdal into python2 conda env
+RUN conda install -y -n python2 \
+gdal \
+basemap \
+landlab -c landlab 
+
+######################
+# SET PATH VARIABLES #
+######################
+
+ENV PATH=/opt/conda/envs/python2/bin:/home/jovyan/libs/TauDEM:$PATH PYTHONPATH=/home/jovyan/work/notebooks/utilities:$PYTHONPATH DOCUMENTS=/home/jovyan/work/notebooks/documents DATA=/home/jovyan/work/notebooks/data HOME=/home/jovyan/work/notebooks ECOHYDROLIB_CFG=/home/jovyan/.ecohydro.cfg LD_LIBRARY_PATH=/usr/lib/grass64/lib
+
+#RUN /bin/bash -c "source /opt/conda/bin/activate python2" && \
+#pip install --upgrade hs_restclient
+
+# install odm2api, then upgrade it to renamevalueobjects branch
+RUN conda install -y -n python2 -c odm2 odm2api
+#RUN /bin/bash -c "source /opt/conda/bin/activate python2 \
+#&& pip install --upgrade --process-dependency-links git+https://github.com/ODM2/ODM2PythonAPI.git@renamevalueobjects"
+
+# prepare grass environment
+#RUN mkdir notebooks
+#ADD create_grass_loc.sh /home/jovyan/libs/create_grass_loc.sh
+ADD rhessys_wf.py /home/jovyan/libs/rhessys_wf.py
+ADD run.py /home/jovyan/libs/run.py
+
+CMD ["sh", "/srv/singleuser/singleuser.sh"]
+
+
+
diff --git a/docker/cleanup.cron → docker/bck/cleanup.cron b/docker/cleanup.cron → docker/bck/cleanup.cron
diff --git a/docker/create_grass_loc.sh → docker/bck/create_grass_loc.sh b/docker/create_grass_loc.sh → docker/bck/create_grass_loc.sh